diff --git a/ChangeLog b/ChangeLog index 9ac6c1ab1..be042ac5a 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,5 +1,10 @@ CHANGES ======= +4.2.5 +----- +* remove if_absent annotations on KL/AT that result in downstream enumeration errors in python dataclasses +representation of the model, see: https://github.com/linkml/linkml/pull/2329 and associated ticket for more details + 4.2.4 ----- * regenerating artifacts diff --git a/Makefile b/Makefile index 70830748f..01bf8d64d 100644 --- a/Makefile +++ b/Makefile @@ -124,7 +124,7 @@ gen-project: $(PYMODEL) -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL) mv $(DEST)/prefixmap/biolink_model.yaml $(DEST)/prefixmap/biolink-model-prefix-map.json mv $(PYMODEL)/biolink*.py $(PYMODEL)/model.py - $(RUN) gen-pydantic src/biolink_model/schema/biolink_model.yaml > $(PYMODEL)/pydanticmodel_v2.py + $(RUN) gen-pydantic --meta None src/biolink_model/schema/biolink_model.yaml > $(PYMODEL)/pydanticmodel_v2.py $(RUN) gen-owl --mergeimports --no-metaclasses --no-type-objects --add-root-classes --mixins-as-expressions src/biolink_model/schema/biolink_model.yaml > $(DEST)/owl/biolink_model.owl.ttl cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml $(MAKE) id-prefixes diff --git a/biolink-model.yaml b/biolink-model.yaml index 2e8f43205..2abfaaec7 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -6138,7 +6138,6 @@ slots: range: KnowledgeLevelEnum multivalued: false required: true - ifabsent: string(not_provided) examples: - value: knowledge_assertion - value: prediction @@ -6166,7 +6165,6 @@ slots: range: AgentTypeEnum multivalued: false required: true - ifabsent: string(not_provided) examples: - value: manual_agent - value: automated_agent diff --git a/poetry.lock b/poetry.lock index 3634f891a..bbb124800 100644 --- a/poetry.lock +++ b/poetry.lock @@ -919,13 +919,13 @@ referencing = ">=0.31.0" [[package]] name = "linkml" -version = "1.7.8" +version = "1.8.4" description = "Linked Open Data Modeling Language" optional = false python-versions = "<4.0.0,>=3.8.1" files = [ - {file = "linkml-1.7.8-py3-none-any.whl", hash = "sha256:4b8ebe33b422517b08ca01802dc2899ac133c502a71d811c58fa6f4263130709"}, - {file = "linkml-1.7.8.tar.gz", hash = "sha256:af48ee1ad6751c8d20de2832dbeefe225da9be5f39a7f8ea7821a691cf7c0148"}, + {file = "linkml-1.8.4-py3-none-any.whl", hash = "sha256:9fa26d7e522dd98568d0313e363abd67c2b17a671f31595c9e53beaec27b7214"}, + {file = "linkml-1.8.4.tar.gz", hash = "sha256:a1918d226ab5c268e260ddc7cfa6edb53d7faab3fb0144efef5fad572b052c36"}, ] [package.dependencies] @@ -938,7 +938,7 @@ jinja2 = ">=3.1.0" jsonasobj2 = ">=1.0.3,<2.0.0" jsonschema = {version = ">=4.0.0", extras = ["format"]} linkml-dataops = "*" -linkml-runtime = ">=1.7.4" +linkml-runtime = ">=1.8.1,<2.0.0" openpyxl = "*" parse = "*" prefixcommons = ">=0.1.7" @@ -956,8 +956,9 @@ watchdog = ">=0.9.0" [package.extras] black = ["black (>=24.0.0)"] +numpydantic = ["numpydantic (>=1.6.1)"] shacl = ["pyshacl (>=0.25.0,<0.26.0)"] -tests = ["black (>=24.0.0)", "pyshacl (>=0.25.0,<0.26.0)"] +tests = ["black (>=24.0.0)", "numpydantic (>=1.6.1)", "pyshacl (>=0.25.0,<0.26.0)"] [[package]] name = "linkml-dataops" @@ -979,13 +980,13 @@ linkml-runtime = ">=1.1.6" [[package]] name = "linkml-runtime" -version = "1.7.5" +version = "1.8.3" description = "Runtime environment for LinkML, the Linked open data modeling language" optional = false python-versions = "<4.0,>=3.8" files = [ - {file = "linkml_runtime-1.7.5-py3-none-any.whl", hash = "sha256:c58000c7c68fa97b7d76c50421a85a64e25f07eec5bcac464bc00c4cd79007a6"}, - {file = "linkml_runtime-1.7.5.tar.gz", hash = "sha256:b31197a5398359441ae1ed43470c54377a1d08db961366dda670300dddcd71d7"}, + {file = "linkml_runtime-1.8.3-py3-none-any.whl", hash = "sha256:0750920f1348fffa903d99e7b5834ce425a2a538285aff9068dbd96d05caabd1"}, + {file = "linkml_runtime-1.8.3.tar.gz", hash = "sha256:5b7f682eef54aaf0a59c50eeacdb11463b43b124a044caf496cde59936ac05c8"}, ] [package.dependencies] diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql index de01934c3..6fd4805f5 100644 --- a/project/graphql/biolink_model.graphql +++ b/project/graphql/biolink_model.graphql @@ -1,3 +1,5 @@ +# metamodel_version: 1.7.0 +# version: 4.2.4 type AccessibleDnaRegion implements GenomicEntity, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, OntologyClass { id: String! diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld index 4a360a598..07f4463f7 100644 --- a/project/jsonld/biolink_model.context.jsonld +++ b/project/jsonld/biolink_model.context.jsonld @@ -1,10 +1,11 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-10-10T17:38:44", + "generation_date": "2024-10-10T16:37:53", "source": "biolink_model.yaml" }, "@context": { + "xsd": "http://www.w3.org/2001/XMLSchema#", "AGRKB": "https://www.alliancegenome.org/", "APO": { "@id": "http://purl.obolibrary.org/obo/APO_", @@ -578,7 +579,6 @@ "@id": "http://www.w3.org/2003/01/geo/wgs84_pos", "@prefix": true }, - "xsd": "http://www.w3.org/2001/XMLSchema#", "@vocab": "https://w3id.org/biolink/vocab/", "active_in": { "@type": "@id", @@ -644,12 +644,11 @@ "@id": "affects_response_to" }, "affiliation": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "affiliation" }, "agent_type": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -733,7 +732,6 @@ }, "available_from": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -790,12 +788,11 @@ "@id": "catalyzes" }, "category": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "category" }, "causal_mechanism_qualifier": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -829,7 +826,6 @@ }, "clinical_approval_status": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1026,7 +1022,6 @@ }, "drug_regulatory_status_world_wide": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1092,7 +1087,6 @@ }, "FDA_adverse_event_level": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1146,7 +1140,6 @@ }, "genome_build": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1469,7 +1462,6 @@ }, "highest_FDA_approval_status": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1643,7 +1635,6 @@ }, "knowledge_level": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1702,7 +1693,6 @@ }, "logical_interpretation": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1722,7 +1712,6 @@ }, "max_research_phase": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1749,7 +1738,7 @@ "@id": "mentions" }, "mesh_terms": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "mesh_terms" }, "missing_from": { @@ -1830,7 +1819,6 @@ }, "object_direction_qualifier": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1877,7 +1865,7 @@ "@id": "original_object" }, "original_predicate": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "original_predicate" }, "original_subject": { @@ -1915,7 +1903,6 @@ }, "phase": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2003,7 +1990,7 @@ "@id": "publications" }, "published_in": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "published_in" }, "publisher": { @@ -2030,7 +2017,6 @@ }, "reaction_direction": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2039,7 +2025,6 @@ }, "reaction_side": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2094,12 +2079,11 @@ "@id": "resistance_associated_with" }, "resource_id": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "resource_id" }, "resource_role": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2131,7 +2115,6 @@ }, "routes_of_delivery": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2204,7 +2187,6 @@ }, "strand": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2245,7 +2227,6 @@ }, "subject_direction_qualifier": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2296,7 +2277,7 @@ "@id": "supporting_document_year" }, "supporting_documents": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "supporting_documents" }, "supporting_study_cohort": { @@ -2312,11 +2293,11 @@ "@id": "supporting_study_metadata" }, "supporting_study_method_description": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "supporting_study_method_description" }, "supporting_study_method_type": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "supporting_study_method_type" }, "supporting_study_size": { @@ -2421,7 +2402,7 @@ "@id": "update_date" }, "upstream_resource_ids": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "upstream_resource_ids" }, "url": { @@ -2446,7 +2427,7 @@ "@id": "xenologous_to" }, "xref": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "xref" }, "AccessibleDnaRegion": { diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld index 86421c367..2a4d139e7 100644 --- a/project/jsonld/biolink_model.jsonld +++ b/project/jsonld/biolink_model.jsonld @@ -2058,12 +2058,12 @@ ], "domain": "Entity", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", - "multivalued": true, "owner": "Entity", "domain_of": [ "Entity" ], "range": "Attribute", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2123,13 +2123,13 @@ ], "domain": "Attribute", "slot_uri": "https://w3id.org/biolink/vocab/has_quantitative_value", - "multivalued": true, "owner": "ChemicalExposure", "domain_of": [ "Attribute", "ChemicalExposure" ], "range": "QuantityValue", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -2271,12 +2271,12 @@ ], "domain": "Entity", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "multivalued": true, "owner": "Entity", "domain_of": [ "Entity" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2290,7 +2290,6 @@ "is_a": "type", "domain": "Entity", "slot_uri": "https://w3id.org/biolink/vocab/category", - "multivalued": true, "designates_type": true, "owner": "Entity", "domain_of": [ @@ -2298,6 +2297,7 @@ ], "is_class_field": true, "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2316,12 +2316,12 @@ "WIKIDATA" ], "slot_uri": "http://purl.org/dc/terms/type", - "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2461,13 +2461,13 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/synonym", - "multivalued": true, "owner": "GeneProductMixin", "domain_of": [ "NamedThing", "GeneProductMixin" ], "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2480,9 +2480,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/exact_synonym", - "multivalued": true, "owner": "exact_synonym", "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2495,9 +2495,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/broad_synonym", - "multivalued": true, "owner": "broad_synonym", "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2510,9 +2510,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/narrow_synonym", - "multivalued": true, "owner": "narrow_synonym", "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2525,9 +2525,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_synonym", - "multivalued": true, "owner": "related_synonym", "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2586,7 +2586,6 @@ ], "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/xref", - "multivalued": true, "owner": "GeneProductMixin", "domain_of": [ "NamedThing", @@ -2596,6 +2595,7 @@ "GeneProductMixin" ], "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2636,9 +2636,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/support_graphs", - "multivalued": true, "owner": "support_graphs", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2686,12 +2686,12 @@ ], "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/retrieval_source_ids", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "RetrievalSource", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2764,9 +2764,9 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "http://purl.obolibrary.org/obo/go#systematic_synonym", - "multivalued": true, "owner": "systematic_synonym", "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2777,12 +2777,12 @@ "is_a": "node_property", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/affiliation", - "multivalued": true, "owner": "Agent", "domain_of": [ "Agent" ], "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3272,12 +3272,12 @@ "is_a": "node_property", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/authors", - "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3348,12 +3348,12 @@ "is_a": "node_property", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/pages", - "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3386,12 +3386,12 @@ "is_a": "node_property", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/keywords", - "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3408,12 +3408,12 @@ ], "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/mesh_terms", - "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3440,12 +3440,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_gene_or_gene_product", - "multivalued": true, "owner": "GeneGroupingMixin", "domain_of": [ "GeneGroupingMixin" ], "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3456,12 +3456,12 @@ "is_a": "has_gene_or_gene_product", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_gene", - "multivalued": true, "owner": "SequenceVariant", "domain_of": [ "SequenceVariant" ], "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3519,9 +3519,9 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_constituent", - "multivalued": true, "owner": "has_constituent", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3532,12 +3532,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_drug", - "multivalued": true, "owner": "Treatment", "domain_of": [ "Treatment" ], "range": "Drug", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3548,12 +3548,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_device", - "multivalued": true, "owner": "Treatment", "domain_of": [ "Treatment" ], "range": "Device", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3564,12 +3564,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_procedure", - "multivalued": true, "owner": "Treatment", "domain_of": [ "Treatment" ], "range": "Procedure", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3706,12 +3706,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/available_from", - "multivalued": true, "owner": "ChemicalEntity", "domain_of": [ "ChemicalEntity" ], "range": "DrugAvailabilityEnum", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3743,13 +3743,13 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_chemical_role", - "multivalued": true, "inherited": true, "owner": "ChemicalEntity", "domain_of": [ "ChemicalEntity" ], "range": "ChemicalRole", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3775,9 +3775,9 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/animal_model_available_from", - "multivalued": true, "owner": "animal_model_available_from", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3856,12 +3856,12 @@ "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/routes_of_delivery", - "multivalued": true, "owner": "ChemicalMixture", "domain_of": [ "ChemicalMixture" ], "range": "DrugDeliveryEnum", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4054,12 +4054,12 @@ "description": "A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/predicate_mappings", - "multivalued": true, "owner": "MappingCollection", "domain_of": [ "MappingCollection" ], "range": "PredicateMapping", + "multivalued": true, "inlined": true, "inlined_as_list": true, "@type": "SlotDefinition" @@ -4070,8 +4070,8 @@ "description": "A list of terms from different schemas or terminology systems that have an identical meaning. Such terms often describe the same concept from different ontological perspectives.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/exact_matches", - "multivalued": true, "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4080,8 +4080,8 @@ "description": "A list of terms from different schemas or terminology systems that have a narrower meaning. Such terms often describe a more specific concept from different ontological perspectives.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/narrow_matches", - "multivalued": true, "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4090,8 +4090,8 @@ "description": "A list of terms from different schemas or terminology systems that have a broader meaning. Such terms often describe a more general concept from different ontological perspectives.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/broad_matches", - "multivalued": true, "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4590,12 +4590,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/qualifiers", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4727,12 +4727,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/catalyst_qualifier", - "multivalued": true, "owner": "ChemicalToChemicalDerivationAssociation", "domain_of": [ "ChemicalToChemicalDerivationAssociation" ], "range": "MacromolecularMachineMixin", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -4891,11 +4891,11 @@ ], "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_to", - "multivalued": true, "inherited": true, "owner": "related_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4913,11 +4913,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_to_at_concept_level", - "multivalued": true, "inherited": true, "owner": "related_to_at_concept_level", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4935,11 +4935,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_to_at_instance_level", - "multivalued": true, "inherited": true, "owner": "related_to_at_instance_level", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4961,11 +4961,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with", - "multivalued": true, "inherited": true, "owner": "associated_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4995,11 +4995,11 @@ "is_a": "related_to_at_concept_level", "domain": "OntologyClass", "slot_uri": "https://w3id.org/biolink/vocab/superclass_of", - "multivalued": true, "inherited": true, "owner": "superclass_of", "inverse": "subclass_of", "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5053,11 +5053,11 @@ "is_a": "related_to_at_concept_level", "domain": "OntologyClass", "slot_uri": "https://w3id.org/biolink/vocab/subclass_of", - "multivalued": true, "inherited": true, "owner": "subclass_of", "inverse": "superclass_of", "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5091,11 +5091,11 @@ "is_a": "exact_match", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/same_as", - "multivalued": true, "inherited": true, "owner": "same_as", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5128,11 +5128,11 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/close_match", - "multivalued": true, "inherited": true, "owner": "close_match", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5158,7 +5158,6 @@ "is_a": "close_match", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/exact_match", - "multivalued": true, "inherited": true, "owner": "PredicateMapping", "domain_of": [ @@ -5166,6 +5165,7 @@ ], "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5195,7 +5195,6 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/broad_match", - "multivalued": true, "inherited": true, "owner": "PredicateMapping", "domain_of": [ @@ -5203,6 +5202,7 @@ ], "inverse": "narrow_match", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5227,7 +5227,6 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/narrow_match", - "multivalued": true, "inherited": true, "owner": "PredicateMapping", "domain_of": [ @@ -5235,6 +5234,7 @@ ], "inverse": "broad_match", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5254,11 +5254,11 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/member_of", - "multivalued": true, "inherited": true, "owner": "member_of", "inverse": "has_member", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5276,11 +5276,11 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_member", - "multivalued": true, "inherited": true, "owner": "has_member", "inverse": "member_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5305,11 +5305,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/opposite_of", - "multivalued": true, "inherited": true, "owner": "opposite_of", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5333,11 +5333,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/affects_likelihood_of", - "multivalued": true, "inherited": true, "owner": "affects_likelihood_of", "inverse": "likelihood_affected_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5347,11 +5347,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/likelihood_affected_by", - "multivalued": true, "inherited": true, "owner": "likelihood_affected_by", "inverse": "affects_likelihood_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5369,11 +5369,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_likelihood_of", - "multivalued": true, "inherited": true, "owner": "associated_with_likelihood_of", "inverse": "likelihood_associated_with", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5384,11 +5384,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/likelihood_associated_with", - "multivalued": true, "inherited": true, "owner": "likelihood_associated_with", "inverse": "associated_with_likelihood_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5406,11 +5406,11 @@ "is_a": "associated_with_likelihood_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_increased_likelihood_of", - "multivalued": true, "inherited": true, "owner": "associated_with_increased_likelihood_of", "inverse": "increased_likelihood_associated_with", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5421,11 +5421,11 @@ "is_a": "likelihood_associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/increased_likelihood_associated_with", - "multivalued": true, "inherited": true, "owner": "increased_likelihood_associated_with", "inverse": "associated_with_increased_likelihood_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5443,11 +5443,11 @@ "is_a": "associated_with_likelihood_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_decreased_likelihood_of", - "multivalued": true, "inherited": true, "owner": "associated_with_decreased_likelihood_of", "inverse": "decreased_likelihood_associated_with", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5458,11 +5458,11 @@ "is_a": "likelihood_associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/decreased_likelihood_associated_with", - "multivalued": true, "inherited": true, "owner": "decreased_likelihood_associated_with", "inverse": "associated_with_decreased_likelihood_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5480,11 +5480,11 @@ "is_a": "related_to_at_instance_level", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/target_for", - "multivalued": true, "inherited": true, "owner": "target_for", "inverse": "has_target", "range": "Disease", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5494,11 +5494,11 @@ "is_a": "related_to_at_instance_level", "domain": "Disease", "slot_uri": "https://w3id.org/biolink/vocab/has_target", - "multivalued": true, "inherited": true, "owner": "has_target", "inverse": "target_for", "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5518,11 +5518,11 @@ "is_a": "related_to_at_instance_level", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/active_in", - "multivalued": true, "inherited": true, "owner": "active_in", "inverse": "has_active_component", "range": "CellularComponent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5532,11 +5532,11 @@ "is_a": "related_to_at_instance_level", "domain": "CellularComponent", "slot_uri": "https://w3id.org/biolink/vocab/has_active_component", - "multivalued": true, "inherited": true, "owner": "has_active_component", "inverse": "active_in", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5557,11 +5557,11 @@ "is_a": "related_to_at_instance_level", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of", "inverse": "has_upstream_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5571,11 +5571,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_upstream_actor", - "multivalued": true, "inherited": true, "owner": "has_upstream_actor", "inverse": "acts_upstream_of", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5596,11 +5596,11 @@ "is_a": "acts_upstream_of", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_positive_effect", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of_positive_effect", "inverse": "has_positive_upstream_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5610,11 +5610,11 @@ "is_a": "has_upstream_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_positive_upstream_actor", - "multivalued": true, "inherited": true, "owner": "has_positive_upstream_actor", "inverse": "acts_upstream_of_positive_effect", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5635,11 +5635,11 @@ "is_a": "acts_upstream_of", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_negative_effect", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of_negative_effect", "inverse": "has_negative_upstream_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5649,11 +5649,11 @@ "is_a": "has_upstream_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_negative_upstream_actor", - "multivalued": true, "inherited": true, "owner": "has_negative_upstream_actor", "inverse": "acts_upstream_of_negative_effect", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5674,11 +5674,11 @@ "is_a": "acts_upstream_of", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_or_within", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of_or_within", "inverse": "has_upstream_or_within_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5688,11 +5688,11 @@ "is_a": "has_upstream_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_upstream_or_within_actor", - "multivalued": true, "inherited": true, "owner": "has_upstream_or_within_actor", "inverse": "acts_upstream_of_or_within", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5713,11 +5713,11 @@ "is_a": "acts_upstream_of_or_within", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_or_within_positive_effect", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of_or_within_positive_effect", "inverse": "has_positive_upstream_or_within_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5727,11 +5727,11 @@ "is_a": "has_upstream_or_within_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_positive_upstream_or_within_actor", - "multivalued": true, "inherited": true, "owner": "has_positive_upstream_or_within_actor", "inverse": "acts_upstream_of_or_within_positive_effect", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5752,11 +5752,11 @@ "is_a": "acts_upstream_of_or_within", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_or_within_negative_effect", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of_or_within_negative_effect", "inverse": "has_negative_upstream_or_within_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5766,11 +5766,11 @@ "is_a": "has_upstream_or_within_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_negative_upstream_or_within_actor", - "multivalued": true, "inherited": true, "owner": "has_negative_upstream_or_within_actor", "inverse": "acts_upstream_of_or_within_negative_effect", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5788,11 +5788,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/mentions", - "multivalued": true, "inherited": true, "owner": "mentions", "inverse": "mentioned_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5803,11 +5803,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/mentioned_by", - "multivalued": true, "inherited": true, "owner": "mentioned_by", "inverse": "mentions", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5824,11 +5824,11 @@ "abstract": true, "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/contributor", - "multivalued": true, "inherited": true, "owner": "contributor", "inverse": "has_contributor", "range": "InformationContentEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5838,11 +5838,11 @@ "is_a": "related_to_at_instance_level", "domain": "InformationContentEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_contributor", - "multivalued": true, "inherited": true, "owner": "has_contributor", "inverse": "contributor", "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5853,11 +5853,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/provider", - "multivalued": true, "inherited": true, "owner": "provider", "inverse": "has_provider", "range": "InformationContentEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5867,11 +5867,11 @@ "is_a": "has_contributor", "domain": "InformationContentEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_provider", - "multivalued": true, "inherited": true, "owner": "has_provider", "inverse": "provider", "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5886,11 +5886,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/publisher", - "multivalued": true, "inherited": true, "owner": "publisher", "inverse": "has_publisher", "range": "Publication", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5900,11 +5900,11 @@ "is_a": "has_contributor", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/has_publisher", - "multivalued": true, "inherited": true, "owner": "has_publisher", "inverse": "publisher", "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5918,11 +5918,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/editor", - "multivalued": true, "inherited": true, "owner": "editor", "inverse": "has_editor", "range": "Publication", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5932,11 +5932,11 @@ "is_a": "has_contributor", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/has_editor", - "multivalued": true, "inherited": true, "owner": "has_editor", "inverse": "editor", "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5951,11 +5951,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/author", - "multivalued": true, "inherited": true, "owner": "author", "inverse": "has_author", "range": "Publication", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5965,11 +5965,11 @@ "is_a": "has_contributor", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/has_author", - "multivalued": true, "inherited": true, "owner": "has_author", "inverse": "author", "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5990,11 +5990,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/assesses", - "multivalued": true, "inherited": true, "owner": "assesses", "inverse": "is_assessed_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6004,11 +6004,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/is_assessed_by", - "multivalued": true, "inherited": true, "owner": "is_assessed_by", "inverse": "assesses", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6029,11 +6029,11 @@ "mixin": true, "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/interacts_with", - "multivalued": true, "inherited": true, "owner": "interacts_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6075,11 +6075,11 @@ ], "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/physically_interacts_with", - "multivalued": true, "inherited": true, "owner": "physically_interacts_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6110,11 +6110,11 @@ "is_a": "physically_interacts_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/directly_physically_interacts_with", - "multivalued": true, "inherited": true, "owner": "directly_physically_interacts_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6136,11 +6136,11 @@ "is_a": "directly_physically_interacts_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/binds", - "multivalued": true, "inherited": true, "owner": "binds", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6157,11 +6157,11 @@ "is_a": "physically_interacts_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/indirectly_physically_interacts_with", - "multivalued": true, "inherited": true, "owner": "indirectly_physically_interacts_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6185,11 +6185,11 @@ "is_a": "interacts_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/genetically_interacts_with", - "multivalued": true, "inherited": true, "owner": "genetically_interacts_with", "symmetric": true, "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6210,11 +6210,11 @@ "is_a": "genetically_interacts_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/gene_fusion_with", - "multivalued": true, "inherited": true, "owner": "gene_fusion_with", "symmetric": true, "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6235,11 +6235,11 @@ "is_a": "genetically_interacts_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/genetic_neighborhood_of", - "multivalued": true, "inherited": true, "owner": "genetic_neighborhood_of", "symmetric": true, "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6302,11 +6302,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/affects", - "multivalued": true, "inherited": true, "owner": "affects", "inverse": "affected_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6317,11 +6317,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/affected_by", - "multivalued": true, "inherited": true, "owner": "affected_by", "inverse": "affects", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6345,11 +6345,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_sensitivity_to", - "multivalued": true, "inherited": true, "owner": "associated_with_sensitivity_to", "inverse": "sensitivity_associated_with", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6359,11 +6359,11 @@ "is_a": "associated_with", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/sensitivity_associated_with", - "multivalued": true, "inherited": true, "owner": "sensitivity_associated_with", "inverse": "associated_with_sensitivity_to", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6381,11 +6381,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_resistance_to", - "multivalued": true, "inherited": true, "owner": "associated_with_resistance_to", "inverse": "resistance_associated_with", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6395,11 +6395,11 @@ "is_a": "associated_with", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/resistance_associated_with", - "multivalued": true, "inherited": true, "owner": "resistance_associated_with", "inverse": "associated_with_resistance_to", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6425,11 +6425,11 @@ "is_a": "related_to_at_instance_level", "domain": "DiagnosticAid", "slot_uri": "https://w3id.org/biolink/vocab/diagnoses", - "multivalued": true, "inherited": true, "owner": "diagnoses", "inverse": "is_diagnosed_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6439,11 +6439,11 @@ "is_a": "related_to_at_instance_level", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/is_diagnosed_by", - "multivalued": true, "inherited": true, "owner": "is_diagnosed_by", "inverse": "diagnoses", "range": "DiagnosticAid", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6456,11 +6456,11 @@ "mixin": true, "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/increases_amount_or_activity_of", - "multivalued": true, "inherited": true, "owner": "increases_amount_or_activity_of", "inverse": "amount_or_activity_increased_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6471,11 +6471,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/amount_or_activity_increased_by", - "multivalued": true, "inherited": true, "owner": "amount_or_activity_increased_by", "inverse": "increases_amount_or_activity_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6488,11 +6488,11 @@ "mixin": true, "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/decreases_amount_or_activity_of", - "multivalued": true, "inherited": true, "owner": "decreases_amount_or_activity_of", "inverse": "amount_or_activity_decreased_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6503,11 +6503,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/amount_or_activity_decreased_by", - "multivalued": true, "inherited": true, "owner": "amount_or_activity_decreased_by", "inverse": "decreases_amount_or_activity_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6556,11 +6556,11 @@ "is_a": "affects", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/affects_response_to", - "multivalued": true, "inherited": true, "owner": "affects_response_to", "inverse": "response_affected_by", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6575,11 +6575,11 @@ "is_a": "affected_by", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/response_affected_by", - "multivalued": true, "inherited": true, "owner": "response_affected_by", "inverse": "affects_response_to", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6609,11 +6609,11 @@ "is_a": "affects_response_to", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/increases_response_to", - "multivalued": true, "inherited": true, "owner": "increases_response_to", "inverse": "response_increased_by", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6627,11 +6627,11 @@ "is_a": "response_affected_by", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/response_increased_by", - "multivalued": true, "inherited": true, "owner": "response_increased_by", "inverse": "increases_response_to", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6664,11 +6664,11 @@ "is_a": "affects_response_to", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/decreases_response_to", - "multivalued": true, "inherited": true, "owner": "decreases_response_to", "inverse": "response_decreased_by", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6682,11 +6682,11 @@ "is_a": "response_affected_by", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/response_decreased_by", - "multivalued": true, "inherited": true, "owner": "response_decreased_by", "inverse": "decreases_response_to", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6721,11 +6721,11 @@ ], "domain": "PhysicalEssenceOrOccurrent", "slot_uri": "https://w3id.org/biolink/vocab/regulates", - "multivalued": true, "inherited": true, "owner": "regulates", "inverse": "regulated_by", "range": "PhysicalEssenceOrOccurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6736,11 +6736,11 @@ "is_a": "affected_by", "domain": "PhysicalEssenceOrOccurrent", "slot_uri": "https://w3id.org/biolink/vocab/regulated_by", - "multivalued": true, "inherited": true, "owner": "regulated_by", "inverse": "regulates", "range": "PhysicalEssenceOrOccurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6778,11 +6778,11 @@ "is_a": "affects", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disrupts", - "multivalued": true, "inherited": true, "owner": "disrupts", "inverse": "disrupted_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6793,11 +6793,11 @@ "is_a": "affected_by", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disrupted_by", - "multivalued": true, "inherited": true, "owner": "disrupted_by", "inverse": "disrupts", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6821,11 +6821,11 @@ "is_a": "related_to_at_instance_level", "domain": "GeneProductMixin", "slot_uri": "https://w3id.org/biolink/vocab/gene_product_of", - "multivalued": true, "inherited": true, "owner": "gene_product_of", "inverse": "has_gene_product", "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6850,11 +6850,11 @@ "is_a": "related_to_at_instance_level", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/has_gene_product", - "multivalued": true, "inherited": true, "owner": "has_gene_product", "inverse": "gene_product_of", "range": "GeneProductMixin", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6870,11 +6870,11 @@ "is_a": "related_to_at_instance_level", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/transcribed_to", - "multivalued": true, "inherited": true, "owner": "transcribed_to", "inverse": "transcribed_from", "range": "Transcript", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6896,11 +6896,11 @@ "is_a": "related_to_at_instance_level", "domain": "Transcript", "slot_uri": "https://w3id.org/biolink/vocab/transcribed_from", - "multivalued": true, "inherited": true, "owner": "transcribed_from", "inverse": "transcribed_to", "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6922,11 +6922,11 @@ "is_a": "related_to_at_instance_level", "domain": "Transcript", "slot_uri": "https://w3id.org/biolink/vocab/translates_to", - "multivalued": true, "inherited": true, "owner": "translates_to", "inverse": "translation_of", "range": "Protein", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6941,11 +6941,11 @@ "is_a": "related_to_at_instance_level", "domain": "Protein", "slot_uri": "https://w3id.org/biolink/vocab/translation_of", - "multivalued": true, "inherited": true, "owner": "translation_of", "inverse": "translates_to", "range": "Transcript", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6979,11 +6979,11 @@ "is_a": "similar_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/homologous_to", - "multivalued": true, "inherited": true, "owner": "homologous_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7007,11 +7007,11 @@ "is_a": "homologous_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/paralogous_to", - "multivalued": true, "inherited": true, "owner": "paralogous_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7036,11 +7036,11 @@ "is_a": "homologous_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/orthologous_to", - "multivalued": true, "inherited": true, "owner": "orthologous_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7064,11 +7064,11 @@ "is_a": "homologous_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/xenologous_to", - "multivalued": true, "inherited": true, "owner": "xenologous_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7260,11 +7260,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/coexists_with", - "multivalued": true, "inherited": true, "owner": "coexists_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7288,11 +7288,11 @@ "is_a": "coexists_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/in_pathway_with", - "multivalued": true, "inherited": true, "owner": "in_pathway_with", "symmetric": true, "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7320,11 +7320,11 @@ "is_a": "coexists_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/in_complex_with", - "multivalued": true, "inherited": true, "owner": "in_complex_with", "symmetric": true, "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7346,11 +7346,11 @@ "is_a": "coexists_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/in_cell_population_with", - "multivalued": true, "inherited": true, "owner": "in_cell_population_with", "symmetric": true, "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7375,11 +7375,11 @@ "is_a": "coexists_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/colocalizes_with", - "multivalued": true, "inherited": true, "owner": "colocalizes_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7391,11 +7391,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/genetic_association", - "multivalued": true, "inherited": true, "owner": "genetic_association", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7424,11 +7424,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/genetically_associated_with", - "multivalued": true, "inherited": true, "owner": "genetically_associated_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7458,11 +7458,11 @@ "is_a": "genetically_associated_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/gene_associated_with_condition", - "multivalued": true, "inherited": true, "owner": "gene_associated_with_condition", "inverse": "condition_associated_with_gene", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7483,11 +7483,11 @@ "is_a": "genetically_associated_with", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_associated_with_gene", - "multivalued": true, "inherited": true, "owner": "condition_associated_with_gene", "inverse": "gene_associated_with_condition", "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7520,11 +7520,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/contributes_to", - "multivalued": true, "inherited": true, "owner": "contributes_to", "inverse": "contribution_from", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7537,11 +7537,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/contribution_from", - "multivalued": true, "inherited": true, "owner": "contribution_from", "inverse": "contributes_to", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7598,11 +7598,11 @@ "is_a": "contributes_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/causes", - "multivalued": true, "inherited": true, "owner": "causes", "inverse": "caused_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7633,11 +7633,11 @@ "is_a": "contribution_from", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/caused_by", - "multivalued": true, "inherited": true, "owner": "caused_by", "inverse": "causes", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7674,11 +7674,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/ameliorates_condition", - "multivalued": true, "inherited": true, "owner": "ameliorates_condition", "inverse": "condition_ameliorated_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7688,11 +7688,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_ameliorated_by", - "multivalued": true, "inherited": true, "owner": "condition_ameliorated_by", "inverse": "ameliorates_condition", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7729,11 +7729,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/preventative_for_condition", - "multivalued": true, "inherited": true, "owner": "preventative_for_condition", "inverse": "condition_prevented_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7743,11 +7743,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_prevented_by", - "multivalued": true, "inherited": true, "owner": "condition_prevented_by", "inverse": "preventative_for_condition", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7775,11 +7775,11 @@ "mixin": true, "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/promotes_condition", - "multivalued": true, "inherited": true, "owner": "promotes_condition", "inverse": "condition_promoted_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7790,11 +7790,11 @@ "mixin": true, "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_promoted_by", - "multivalued": true, "inherited": true, "owner": "condition_promoted_by", "inverse": "promotes_condition", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7825,11 +7825,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/predisposes_to_condition", - "multivalued": true, "inherited": true, "owner": "predisposes_to_condition", "inverse": "condition_predisposed_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7839,11 +7839,11 @@ "is_a": "likelihood_affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_predisposed_by", - "multivalued": true, "inherited": true, "owner": "condition_predisposed_by", "inverse": "predisposes_to_condition", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7880,11 +7880,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/exacerbates_condition", - "multivalued": true, "inherited": true, "owner": "exacerbates_condition", "inverse": "condition_exacerbated_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7897,11 +7897,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_exacerbated_by", - "multivalued": true, "inherited": true, "owner": "condition_exacerbated_by", "inverse": "exacerbates_condition", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7966,11 +7966,11 @@ "mixin": true, "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/treats", - "multivalued": true, "inherited": true, "owner": "treats", "inverse": "treated_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7991,11 +7991,11 @@ "mixin": true, "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treated_by", - "multivalued": true, "inherited": true, "owner": "treated_by", "inverse": "treats", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8020,11 +8020,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/studied_to_treat", - "multivalued": true, "inherited": true, "owner": "studied_to_treat", "inverse": "treated_in_studies_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8051,11 +8051,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/in_clinical_trials_for", - "multivalued": true, "inherited": true, "owner": "in_clinical_trials_for", "inverse": "tested_by_clinical_trials_of", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8068,11 +8068,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/tested_by_clinical_trials_of", - "multivalued": true, "inherited": true, "owner": "tested_by_clinical_trials_of", "inverse": "in_clinical_trials_for", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8086,11 +8086,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treated_in_studies_by", - "multivalued": true, "inherited": true, "owner": "treated_in_studies_by", "inverse": "studied_to_treat", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8104,11 +8104,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/tested_by_preclinical_trials_of", - "multivalued": true, "inherited": true, "owner": "tested_by_preclinical_trials_of", "inverse": "in_preclinical_trials_for", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8133,11 +8133,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/in_preclinical_trials_for", - "multivalued": true, "inherited": true, "owner": "in_preclinical_trials_for", "inverse": "tested_by_preclinical_trials_of", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8164,11 +8164,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/beneficial_in_models_for", - "multivalued": true, "inherited": true, "owner": "beneficial_in_models_for", "inverse": "models_demonstrating_benefits_for", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8181,11 +8181,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/models_demonstrating_benefits_for", - "multivalued": true, "inherited": true, "owner": "models_demonstrating_benefits_for", "inverse": "beneficial_in_models_for", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8218,11 +8218,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/applied_to_treat", - "multivalued": true, "inherited": true, "owner": "applied_to_treat", "inverse": "treatment_applications_from", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8235,11 +8235,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treatment_applications_from", - "multivalued": true, "inherited": true, "owner": "treatment_applications_from", "inverse": "applied_to_treat", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8268,11 +8268,11 @@ "mixin": true, "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/treats_or_applied_or_studied_to_treat", - "multivalued": true, "inherited": true, "owner": "treats_or_applied_or_studied_to_treat", "inverse": "subject_of_treatment_application_or_study_for_treatment_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8283,11 +8283,11 @@ "mixin": true, "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/subject_of_treatment_application_or_study_for_treatment_by", - "multivalued": true, "inherited": true, "owner": "subject_of_treatment_application_or_study_for_treatment_by", "inverse": "treats_or_applied_or_studied_to_treat", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8316,11 +8316,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/correlated_with", - "multivalued": true, "inherited": true, "owner": "correlated_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8349,11 +8349,11 @@ "is_a": "correlated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/positively_correlated_with", - "multivalued": true, "inherited": true, "owner": "positively_correlated_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8382,11 +8382,11 @@ "is_a": "correlated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/negatively_correlated_with", - "multivalued": true, "inherited": true, "owner": "negatively_correlated_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8407,11 +8407,11 @@ "is_a": "correlated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/occurs_together_in_literature_with", - "multivalued": true, "inherited": true, "owner": "occurs_together_in_literature_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8429,11 +8429,11 @@ "is_a": "correlated_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/coexpressed_with", - "multivalued": true, "inherited": true, "owner": "coexpressed_with", "symmetric": true, "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8452,11 +8452,11 @@ "is_a": "correlated_with", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/has_biomarker", - "multivalued": true, "inherited": true, "owner": "has_biomarker", "inverse": "biomarker_for", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8490,11 +8490,11 @@ "is_a": "correlated_with", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/biomarker_for", - "multivalued": true, "inherited": true, "owner": "biomarker_for", "inverse": "has_biomarker", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8522,11 +8522,11 @@ "is_a": "located_in", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/expressed_in", - "multivalued": true, "inherited": true, "owner": "expressed_in", "inverse": "expresses", "range": "AnatomicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8546,11 +8546,11 @@ "is_a": "location_of", "domain": "AnatomicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/expresses", - "multivalued": true, "inherited": true, "owner": "expresses", "inverse": "expressed_in", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8591,11 +8591,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_phenotype", - "multivalued": true, "inherited": true, "owner": "has_phenotype", "inverse": "phenotype_of", "range": "PhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8605,11 +8605,11 @@ "is_a": "related_to_at_instance_level", "domain": "PhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/phenotype_of", - "multivalued": true, "inherited": true, "owner": "phenotype_of", "inverse": "has_phenotype", "range": "BiologicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8652,11 +8652,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/occurs_in", - "multivalued": true, "inherited": true, "owner": "occurs_in", "inverse": "contains_process", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8666,11 +8666,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/contains_process", - "multivalued": true, "inherited": true, "owner": "contains_process", "inverse": "occurs_in", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8738,11 +8738,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/located_in", - "multivalued": true, "inherited": true, "owner": "located_in", "inverse": "location_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8769,11 +8769,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/location_of", - "multivalued": true, "inherited": true, "owner": "location_of", "inverse": "located_in", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8788,11 +8788,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disease_has_location", - "multivalued": true, "inherited": true, "owner": "disease_has_location", "inverse": "location_of_disease", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8802,11 +8802,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/location_of_disease", - "multivalued": true, "inherited": true, "owner": "location_of_disease", "inverse": "disease_has_location", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8831,11 +8831,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/similar_to", - "multivalued": true, "inherited": true, "owner": "similar_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8865,11 +8865,11 @@ "is_a": "similar_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/chemically_similar_to", - "multivalued": true, "inherited": true, "owner": "chemically_similar_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8890,11 +8890,11 @@ "is_a": "related_to_at_instance_level", "domain": "NucleicAcidEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_sequence_location", - "multivalued": true, "inherited": true, "owner": "has_sequence_location", "inverse": "sequence_location_of", "range": "NucleicAcidEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8904,11 +8904,11 @@ "is_a": "related_to_at_instance_level", "domain": "NucleicAcidEntity", "slot_uri": "https://w3id.org/biolink/vocab/sequence_location_of", - "multivalued": true, "inherited": true, "owner": "sequence_location_of", "inverse": "has_sequence_location", "range": "NucleicAcidEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8935,11 +8935,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/model_of", - "multivalued": true, "inherited": true, "owner": "model_of", "inverse": "models", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8949,11 +8949,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/models", - "multivalued": true, "inherited": true, "owner": "models", "inverse": "model_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8984,11 +8984,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/overlaps", - "multivalued": true, "inherited": true, "owner": "overlaps", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9053,11 +9053,11 @@ "is_a": "overlaps", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_part", - "multivalued": true, "inherited": true, "owner": "has_part", "inverse": "part_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9081,11 +9081,11 @@ "is_a": "has_part", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_plasma_membrane_part", - "multivalued": true, "inherited": true, "owner": "has_plasma_membrane_part", "inverse": "plasma_membrane_part_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9109,11 +9109,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/composed_primarily_of", - "multivalued": true, "inherited": true, "owner": "composed_primarily_of", "inverse": "primarily_composed_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9123,11 +9123,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/primarily_composed_of", - "multivalued": true, "inherited": true, "owner": "primarily_composed_of", "inverse": "composed_primarily_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9137,11 +9137,11 @@ "is_a": "part_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/plasma_membrane_part_of", - "multivalued": true, "inherited": true, "owner": "plasma_membrane_part_of", "inverse": "has_plasma_membrane_part", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9219,11 +9219,11 @@ "is_a": "overlaps", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/part_of", - "multivalued": true, "inherited": true, "owner": "part_of", "inverse": "has_part", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9268,7 +9268,6 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_input", - "multivalued": true, "inherited": true, "owner": "BiologicalProcessOrActivity", "domain_of": [ @@ -9276,6 +9275,7 @@ ], "inverse": "is_input_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9291,11 +9291,11 @@ "is_a": "participates_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/is_input_of", - "multivalued": true, "inherited": true, "owner": "is_input_of", "inverse": "has_input", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9335,7 +9335,6 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_output", - "multivalued": true, "inherited": true, "owner": "BiologicalProcessOrActivity", "domain_of": [ @@ -9343,6 +9342,7 @@ ], "inverse": "is_output_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9361,11 +9361,11 @@ "is_a": "participates_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/is_output_of", - "multivalued": true, "inherited": true, "owner": "is_output_of", "inverse": "has_output", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9414,11 +9414,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_participant", - "multivalued": true, "inherited": true, "owner": "has_participant", "inverse": "participates_in", "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9439,11 +9439,11 @@ "is_a": "participates_in", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/catalyzes", - "multivalued": true, "inherited": true, "owner": "catalyzes", "inverse": "has_catalyst", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9453,11 +9453,11 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_catalyst", - "multivalued": true, "inherited": true, "owner": "has_catalyst", "inverse": "catalyzes", "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9475,11 +9475,11 @@ "is_a": "has_participant", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/has_substrate", - "multivalued": true, "inherited": true, "owner": "has_substrate", "inverse": "is_substrate_of", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9490,11 +9490,11 @@ "is_a": "participates_in", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/is_substrate_of", - "multivalued": true, "inherited": true, "owner": "is_substrate_of", "inverse": "has_substrate", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9527,11 +9527,11 @@ "is_a": "related_to_at_instance_level", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/participates_in", - "multivalued": true, "inherited": true, "owner": "participates_in", "inverse": "has_participant", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9565,11 +9565,11 @@ "is_a": "participates_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/actively_involved_in", - "multivalued": true, "inherited": true, "owner": "actively_involved_in", "inverse": "actively_involves", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9582,11 +9582,11 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/actively_involves", - "multivalued": true, "inherited": true, "owner": "actively_involves", "inverse": "actively_involved_in", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9614,11 +9614,11 @@ "is_a": "actively_involved_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/capable_of", - "multivalued": true, "inherited": true, "owner": "capable_of", "inverse": "can_be_carried_out_by", "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9629,11 +9629,11 @@ "is_a": "actively_involves", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/can_be_carried_out_by", - "multivalued": true, "inherited": true, "owner": "can_be_carried_out_by", "inverse": "capable_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9657,11 +9657,11 @@ "is_a": "participates_in", "domain": "PhysicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/enables", - "multivalued": true, "inherited": true, "owner": "enables", "inverse": "enabled_by", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9685,7 +9685,6 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/enabled_by", - "multivalued": true, "inherited": true, "owner": "BiologicalProcessOrActivity", "domain_of": [ @@ -9693,6 +9692,7 @@ ], "inverse": "enables", "range": "PhysicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9715,11 +9715,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/derives_into", - "multivalued": true, "inherited": true, "owner": "derives_into", "inverse": "derives_from", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9750,11 +9750,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/derives_from", - "multivalued": true, "inherited": true, "owner": "derives_from", "inverse": "derives_into", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9774,11 +9774,11 @@ "is_a": "derives_from", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/is_metabolite_of", - "multivalued": true, "inherited": true, "owner": "is_metabolite_of", "inverse": "has_metabolite", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9805,11 +9805,11 @@ "is_a": "derives_into", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_metabolite", - "multivalued": true, "inherited": true, "owner": "has_metabolite", "inverse": "is_metabolite_of", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9823,11 +9823,11 @@ "is_a": "part_of", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/food_component_of", - "multivalued": true, "inherited": true, "owner": "food_component_of", "inverse": "has_food_component", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9848,11 +9848,11 @@ "is_a": "has_part", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_food_component", - "multivalued": true, "inherited": true, "owner": "has_food_component", "inverse": "food_component_of", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9866,11 +9866,11 @@ "is_a": "food_component_of", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/nutrient_of", - "multivalued": true, "inherited": true, "owner": "nutrient_of", "inverse": "has_nutrient", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9894,11 +9894,11 @@ "is_a": "has_food_component", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_nutrient", - "multivalued": true, "inherited": true, "owner": "has_nutrient", "inverse": "nutrient_of", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9915,11 +9915,11 @@ "is_a": "part_of", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/is_active_ingredient_of", - "multivalued": true, "inherited": true, "owner": "is_active_ingredient_of", "inverse": "has_active_ingredient", "range": "Drug", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9948,11 +9948,11 @@ "is_a": "has_part", "domain": "Drug", "slot_uri": "https://w3id.org/biolink/vocab/has_active_ingredient", - "multivalued": true, "inherited": true, "owner": "has_active_ingredient", "inverse": "is_active_ingredient_of", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9969,11 +9969,11 @@ "is_a": "part_of", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/is_excipient_of", - "multivalued": true, "inherited": true, "owner": "is_excipient_of", "inverse": "has_excipient", "range": "Drug", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9997,11 +9997,11 @@ "is_a": "has_part", "domain": "Drug", "slot_uri": "https://w3id.org/biolink/vocab/has_excipient", - "multivalued": true, "inherited": true, "owner": "has_excipient", "inverse": "is_excipient_of", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10032,11 +10032,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/manifestation_of", - "multivalued": true, "inherited": true, "owner": "manifestation_of", "inverse": "has_manifestation", "range": "Disease", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10046,11 +10046,11 @@ "is_a": "related_to_at_instance_level", "domain": "Disease", "slot_uri": "https://w3id.org/biolink/vocab/has_manifestation", - "multivalued": true, "inherited": true, "owner": "has_manifestation", "inverse": "manifestation_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10060,11 +10060,11 @@ "is_a": "manifestation_of", "domain": "GeneticInheritance", "slot_uri": "https://w3id.org/biolink/vocab/mode_of_inheritance_of", - "multivalued": true, "inherited": true, "owner": "mode_of_inheritance_of", "inverse": "has_mode_of_inheritance", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10085,11 +10085,11 @@ "is_a": "has_manifestation", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/has_mode_of_inheritance", - "multivalued": true, "inherited": true, "owner": "has_mode_of_inheritance", "inverse": "mode_of_inheritance_of", "range": "GeneticInheritance", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10123,11 +10123,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/produces", - "multivalued": true, "inherited": true, "owner": "produces", "inverse": "produced_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10140,11 +10140,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/produced_by", - "multivalued": true, "inherited": true, "owner": "produced_by", "inverse": "produces", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10164,11 +10164,11 @@ "is_a": "has_input", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/consumes", - "multivalued": true, "inherited": true, "owner": "consumes", "inverse": "consumed_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10178,11 +10178,11 @@ "is_a": "is_input_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/consumed_by", - "multivalued": true, "inherited": true, "owner": "consumed_by", "inverse": "consumes", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10219,11 +10219,11 @@ "is_a": "related_to_at_instance_level", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/temporally_related_to", - "multivalued": true, "inherited": true, "owner": "temporally_related_to", "symmetric": true, "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10263,11 +10263,11 @@ "is_a": "temporally_related_to", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/precedes", - "multivalued": true, "inherited": true, "owner": "precedes", "inverse": "preceded_by", "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10293,11 +10293,11 @@ "is_a": "temporally_related_to", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/preceded_by", - "multivalued": true, "inherited": true, "owner": "preceded_by", "inverse": "precedes", "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10319,11 +10319,11 @@ "is_a": "has_part", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_variant_part", - "multivalued": true, "inherited": true, "owner": "has_variant_part", "inverse": "variant_part_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10333,11 +10333,11 @@ "is_a": "part_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/variant_part_of", - "multivalued": true, "inherited": true, "owner": "variant_part_of", "inverse": "has_variant_part", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10357,11 +10357,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_condition", - "multivalued": true, "inherited": true, "owner": "related_condition", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10387,11 +10387,11 @@ "is_a": "related_to_at_instance_level", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_sequence_variant_of", - "multivalued": true, "inherited": true, "owner": "is_sequence_variant_of", "inverse": "has_sequence_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10402,11 +10402,11 @@ "is_a": "related_to_at_instance_level", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_sequence_variant", - "multivalued": true, "inherited": true, "owner": "has_sequence_variant", "inverse": "is_sequence_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10427,11 +10427,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_missense_variant_of", - "multivalued": true, "inherited": true, "owner": "is_missense_variant_of", "inverse": "has_missense_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10442,11 +10442,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_missense_variant", - "multivalued": true, "inherited": true, "owner": "has_missense_variant", "inverse": "is_missense_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10467,11 +10467,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_synonymous_variant_of", - "multivalued": true, "inherited": true, "owner": "is_synonymous_variant_of", "inverse": "has_synonymous_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10485,11 +10485,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_synonymous_variant", - "multivalued": true, "inherited": true, "owner": "has_synonymous_variant", "inverse": "is_synonymous_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10510,11 +10510,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_nonsense_variant_of", - "multivalued": true, "inherited": true, "owner": "is_nonsense_variant_of", "inverse": "has_nonsense_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10525,11 +10525,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_nonsense_variant", - "multivalued": true, "inherited": true, "owner": "has_nonsense_variant", "inverse": "is_nonsense_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10555,11 +10555,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_frameshift_variant_of", - "multivalued": true, "inherited": true, "owner": "is_frameshift_variant_of", "inverse": "has_frameshift_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10575,11 +10575,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_frameshift_variant", - "multivalued": true, "inherited": true, "owner": "has_frameshift_variant", "inverse": "is_frameshift_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10600,11 +10600,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_splice_site_variant_of", - "multivalued": true, "inherited": true, "owner": "is_splice_site_variant_of", "inverse": "has_splice_site_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10619,11 +10619,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_splice_site_variant", - "multivalued": true, "inherited": true, "owner": "has_splice_site_variant", "inverse": "is_splice_site_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10641,11 +10641,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_nearby_variant_of", - "multivalued": true, "inherited": true, "owner": "is_nearby_variant_of", "inverse": "has_nearby_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10663,11 +10663,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_nearby_variant", - "multivalued": true, "inherited": true, "owner": "has_nearby_variant", "inverse": "is_nearby_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10685,11 +10685,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_non_coding_variant_of", - "multivalued": true, "inherited": true, "owner": "is_non_coding_variant_of", "inverse": "has_non_coding_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10700,11 +10700,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_non_coding_variant", - "multivalued": true, "inherited": true, "owner": "has_non_coding_variant", "inverse": "is_non_coding_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10726,11 +10726,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disease_has_basis_in", - "multivalued": true, "inherited": true, "owner": "disease_has_basis_in", "inverse": "occurs_in_disease", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10740,11 +10740,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/occurs_in_disease", - "multivalued": true, "inherited": true, "owner": "occurs_in_disease", "inverse": "disease_has_basis_in", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10765,11 +10765,11 @@ "is_a": "affects", "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/has_adverse_event", - "multivalued": true, "inherited": true, "owner": "has_adverse_event", "inverse": "adverse_event_of", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10779,11 +10779,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/adverse_event_of", - "multivalued": true, "inherited": true, "owner": "adverse_event_of", "inverse": "has_adverse_event", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10811,11 +10811,11 @@ "is_a": "affects", "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/has_side_effect", - "multivalued": true, "inherited": true, "owner": "has_side_effect", "inverse": "is_side_effect_of", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10825,11 +10825,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/is_side_effect_of", - "multivalued": true, "inherited": true, "owner": "is_side_effect_of", "inverse": "has_side_effect", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10859,11 +10859,11 @@ "is_a": "related_to_at_instance_level", "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/contraindicated_in", - "multivalued": true, "inherited": true, "owner": "contraindicated_in", "inverse": "has_contraindication", "range": "BiologicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10883,11 +10883,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_contraindication", - "multivalued": true, "inherited": true, "owner": "has_contraindication", "inverse": "contraindicated_in", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10914,11 +10914,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_not_completed", - "multivalued": true, "inherited": true, "owner": "has_not_completed", "inverse": "not_completed_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10928,11 +10928,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/not_completed_by", - "multivalued": true, "inherited": true, "owner": "not_completed_by", "inverse": "has_not_completed", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10958,11 +10958,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_completed", - "multivalued": true, "inherited": true, "owner": "has_completed", "inverse": "completed_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10972,11 +10972,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/completed_by", - "multivalued": true, "inherited": true, "owner": "completed_by", "inverse": "has_completed", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10997,11 +10997,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/in_linkage_disequilibrium_with", - "multivalued": true, "inherited": true, "owner": "in_linkage_disequilibrium_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11026,11 +11026,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_increased_amount", - "multivalued": true, "inherited": true, "owner": "has_increased_amount", "inverse": "increased_amount_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11040,11 +11040,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/increased_amount_of", - "multivalued": true, "inherited": true, "owner": "increased_amount_of", "inverse": "has_increased_amount", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11069,11 +11069,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_decreased_amount", - "multivalued": true, "inherited": true, "owner": "has_decreased_amount", "inverse": "decreased_amount_in", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11083,11 +11083,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/decreased_amount_in", - "multivalued": true, "inherited": true, "owner": "decreased_amount_in", "inverse": "has_decreased_amount", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11116,11 +11116,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/lacks_part", - "multivalued": true, "inherited": true, "owner": "lacks_part", "inverse": "missing_from", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11130,11 +11130,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/missing_from", - "multivalued": true, "inherited": true, "owner": "missing_from", "inverse": "lacks_part", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11166,11 +11166,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/develops_from", - "multivalued": true, "inherited": true, "owner": "develops_from", "inverse": "develops_into", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11180,11 +11180,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/develops_into", - "multivalued": true, "inherited": true, "owner": "develops_into", "inverse": "develops_from", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11219,7 +11219,6 @@ "is_a": "related_to_at_instance_level", "domain": "ThingWithTaxon", "slot_uri": "https://w3id.org/biolink/vocab/in_taxon", - "multivalued": true, "inherited": true, "owner": "ThingWithTaxon", "domain_of": [ @@ -11227,6 +11226,7 @@ ], "inverse": "taxon_of", "range": "OrganismTaxon", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11264,11 +11264,11 @@ "is_a": "related_to_at_instance_level", "domain": "OrganismTaxon", "slot_uri": "https://w3id.org/biolink/vocab/taxon_of", - "multivalued": true, "inherited": true, "owner": "taxon_of", "inverse": "in_taxon", "range": "ThingWithTaxon", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -11293,11 +11293,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_molecular_consequence", - "multivalued": true, "inherited": true, "owner": "has_molecular_consequence", "inverse": "is_molecular_consequence_of", "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11307,11 +11307,11 @@ "is_a": "related_to_at_instance_level", "domain": "OntologyClass", "slot_uri": "https://w3id.org/biolink/vocab/is_molecular_consequence_of", - "multivalued": true, "inherited": true, "owner": "is_molecular_consequence_of", "inverse": "has_molecular_consequence", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11420,12 +11420,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11450,12 +11450,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11538,12 +11538,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_category_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11568,12 +11568,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_category_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11598,12 +11598,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_label_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11632,12 +11632,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_label_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11940,12 +11940,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/has_evidence", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "EvidenceType", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12039,12 +12039,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/provided_by", - "multivalued": true, "owner": "NamedThing", "domain_of": [ "NamedThing" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12076,12 +12076,12 @@ "is_a": "knowledge_source", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/aggregator_knowledge_source", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12095,9 +12095,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_data_source", - "multivalued": true, "owner": "supporting_data_source", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12108,9 +12108,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_data_set", - "multivalued": true, "owner": "supporting_data_set", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12342,9 +12342,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_text", - "multivalued": true, "owner": "supporting_text", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12362,9 +12362,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_documents", - "multivalued": true, "owner": "supporting_documents", "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12381,9 +12381,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_location_in_text", - "multivalued": true, "owner": "subject_location_in_text", "range": "integer", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12400,9 +12400,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_location_in_text", - "multivalued": true, "owner": "object_location_in_text", "range": "integer", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12592,12 +12592,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/publications", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "Publication", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12829,12 +12829,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/has_supporting_studies", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "Study", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12954,7 +12954,6 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/knowledge_level", - "ifabsent": "string(not_provided)", "owner": "Association", "domain_of": [ "Association" @@ -12992,7 +12991,6 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/agent_type", - "ifabsent": "string(not_provided)", "owner": "Association", "domain_of": [ "Association" @@ -13050,7 +13048,6 @@ "is_a": "category", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/category", - "multivalued": true, "designates_type": true, "alias": "category", "owner": "NamedThing", @@ -13062,6 +13059,7 @@ "usage_slot_name": "category", "range": "uriorcurie", "required": true, + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13242,7 +13240,6 @@ ], "domain": "Publication", "slot_uri": "http://purl.org/dc/terms/type", - "multivalued": true, "alias": "publication type", "owner": "Publication", "domain_of": [ @@ -13252,6 +13249,7 @@ "usage_slot_name": "publication type", "range": "string", "required": true, + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13265,7 +13263,6 @@ "is_a": "pages", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/pages", - "multivalued": true, "alias": "pages", "owner": "Publication", "domain_of": [ @@ -13274,6 +13271,7 @@ "is_usage_slot": true, "usage_slot_name": "pages", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13319,7 +13317,6 @@ "is_a": "type", "domain": "Book", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "multivalued": true, "alias": "type", "owner": "Book", "domain_of": [ @@ -13328,6 +13325,7 @@ "is_usage_slot": true, "usage_slot_name": "type", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13400,7 +13398,6 @@ "is_a": "type", "domain": "Serial", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "multivalued": true, "alias": "type", "owner": "Serial", "domain_of": [ @@ -13409,6 +13406,7 @@ "is_usage_slot": true, "usage_slot_name": "type", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13565,7 +13563,6 @@ "is_a": "has_input", "domain": "MolecularActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_input", - "multivalued": true, "inherited": true, "alias": "has input", "owner": "MolecularActivity", @@ -13575,6 +13572,7 @@ "is_usage_slot": true, "usage_slot_name": "has input", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13616,7 +13614,6 @@ "is_a": "has_output", "domain": "MolecularActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_output", - "multivalued": true, "inherited": true, "alias": "has output", "owner": "MolecularActivity", @@ -13626,6 +13623,7 @@ "is_usage_slot": true, "usage_slot_name": "has output", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13650,7 +13648,6 @@ "is_a": "enabled_by", "domain": "MolecularActivity", "slot_uri": "https://w3id.org/biolink/vocab/enabled_by", - "multivalued": true, "inherited": true, "alias": "enabled by", "owner": "MolecularActivity", @@ -13660,6 +13657,7 @@ "is_usage_slot": true, "usage_slot_name": "enabled by", "range": "MacromolecularMachineMixin", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -13756,7 +13754,6 @@ "is_a": "has_attribute", "domain": "OrganismalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", - "multivalued": true, "alias": "has attribute", "owner": "OrganismalEntity", "domain_of": [ @@ -13765,6 +13762,7 @@ "is_usage_slot": true, "usage_slot_name": "has attribute", "range": "Attribute", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13813,7 +13811,6 @@ "is_a": "has_gene", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/has_gene", - "multivalued": true, "alias": "has gene", "owner": "SequenceVariant", "domain_of": [ @@ -13822,6 +13819,7 @@ "is_usage_slot": true, "usage_slot_name": "has gene", "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -14005,7 +14003,6 @@ "is_a": "has_attribute", "domain": "ClinicalFinding", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", - "multivalued": true, "alias": "has attribute", "owner": "ClinicalFinding", "domain_of": [ @@ -14014,6 +14011,7 @@ "is_usage_slot": true, "usage_slot_name": "has attribute", "range": "ClinicalAttribute", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -14109,7 +14107,6 @@ "is_a": "has_attribute", "domain": "SocioeconomicExposure", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", - "multivalued": true, "alias": "has attribute", "owner": "SocioeconomicExposure", "domain_of": [ @@ -14119,6 +14116,7 @@ "usage_slot_name": "has attribute", "range": "SocioeconomicAttribute", "required": true, + "multivalued": true, "@type": "SlotDefinition" }, { @@ -14136,7 +14134,6 @@ "is_a": "type", "domain": "Association", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "multivalued": true, "alias": "type", "owner": "Association", "domain_of": [ @@ -14145,6 +14142,7 @@ "is_usage_slot": true, "usage_slot_name": "type", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -14158,7 +14156,6 @@ "is_a": "category", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/category", - "multivalued": true, "designates_type": true, "alias": "category", "owner": "Association", @@ -14169,6 +14166,7 @@ "is_usage_slot": true, "usage_slot_name": "category", "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -14410,7 +14408,6 @@ "is_a": "qualifiers", "domain": "ContributorAssociation", "slot_uri": "https://w3id.org/biolink/vocab/qualifiers", - "multivalued": true, "alias": "qualifiers", "owner": "ContributorAssociation", "domain_of": [ @@ -14419,6 +14416,7 @@ "is_usage_slot": true, "usage_slot_name": "qualifiers", "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -15767,7 +15765,6 @@ "is_a": "catalyst_qualifier", "domain": "ChemicalToChemicalDerivationAssociation", "slot_uri": "https://w3id.org/biolink/vocab/catalyst_qualifier", - "multivalued": true, "alias": "catalyst qualifier", "owner": "ChemicalToChemicalDerivationAssociation", "domain_of": [ @@ -15776,6 +15773,7 @@ "is_usage_slot": true, "usage_slot_name": "catalyst qualifier", "range": "MacromolecularMachineMixin", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -19790,7 +19788,6 @@ "is_a": "has_evidence", "domain": "DruggableGeneToDiseaseAssociation", "slot_uri": "https://w3id.org/biolink/vocab/has_evidence", - "multivalued": true, "alias": "has evidence", "owner": "DruggableGeneToDiseaseAssociation", "domain_of": [ @@ -19799,6 +19796,7 @@ "is_usage_slot": true, "usage_slot_name": "has evidence", "range": "DruggableGeneCategoryEnum", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -35719,9 +35717,9 @@ ], "metamodel_version": "1.7.0", "source_file": "biolink_model.yaml", - "source_file_date": "2024-10-10T17:38:41", - "source_file_size": 401126, - "generation_date": "2024-10-10T17:38:46", + "source_file_date": "2024-10-10T16:37:48", + "source_file_size": 401056, + "generation_date": "2024-10-10T16:37:55", "@type": "SchemaDefinition", "@context": [ "project/jsonld/biolink_model.context.jsonld", diff --git a/project/jsonschema/biolink_model.schema.json b/project/jsonschema/biolink_model.schema.json index a2f4ad87e..1306a9e67 100644 --- a/project/jsonschema/biolink_model.schema.json +++ b/project/jsonschema/biolink_model.schema.json @@ -16,26 +16,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -46,46 +61,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -111,22 +150,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -134,38 +185,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -181,14 +250,20 @@ "properties": { "address": { "description": "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).", - "type": "string" + "type": [ + "string", + "null" + ] }, "affiliation": { "description": "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -202,22 +277,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.", @@ -225,38 +312,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -297,22 +402,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -323,46 +440,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -378,7 +519,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -389,7 +533,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -399,36 +546,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -436,7 +601,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -444,15 +612,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the structure at an earlier time", @@ -460,48 +637,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -509,32 +713,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the structure at a later time", @@ -542,44 +761,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -599,7 +839,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -610,7 +853,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -620,36 +866,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -657,7 +921,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -665,15 +932,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the whole", @@ -681,48 +957,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -730,32 +1033,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the part", @@ -763,44 +1081,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -845,7 +1184,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -860,29 +1202,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -890,50 +1250,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iso_abbreviation": { "description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", - "type": "string" + "type": [ + "string", + "null" + ] }, "issue": { "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -947,35 +1334,53 @@ "type": "string" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -993,7 +1398,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -1004,7 +1412,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -1014,36 +1425,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1051,7 +1480,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -1059,15 +1491,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -1075,48 +1516,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -1124,32 +1592,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -1157,44 +1640,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1224,22 +1728,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -1247,14 +1763,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1262,38 +1784,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1320,22 +1860,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1346,46 +1898,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1411,43 +1987,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1458,46 +2055,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1513,7 +2134,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -1524,7 +2148,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -1534,55 +2161,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1590,7 +2250,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -1598,15 +2261,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "behavioral feature that is the object of the association", @@ -1614,25 +2286,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -1643,27 +2327,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -1671,40 +2373,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "behavior that is the subject of the association", @@ -1712,25 +2435,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -1741,23 +2476,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1787,22 +2534,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -1810,14 +2569,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1825,43 +2590,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1888,22 +2674,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1914,46 +2712,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1985,43 +2807,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2032,46 +2875,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2097,43 +2964,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2144,46 +3032,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2209,22 +3121,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -2232,14 +3156,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2247,38 +3177,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2305,22 +3253,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -2328,14 +3288,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2343,43 +3309,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2399,7 +3386,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -2414,29 +3404,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Books should have industry-standard identifier such as from ISBN.", @@ -2444,42 +3452,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -2489,32 +3518,47 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "description": "Should generally be set to an ontology class defined term for 'book'.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2534,7 +3578,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -2548,34 +3595,55 @@ }, "chapter": { "description": "chapter of a book", - "type": "string" + "type": [ + "string", + "null" + ] }, "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -2583,42 +3651,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -2632,35 +3721,53 @@ "type": "string" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2688,22 +3795,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2714,46 +3833,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2769,7 +3912,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -2780,7 +3926,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -2790,55 +3939,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2846,7 +4028,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -2854,15 +4039,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -2870,25 +4064,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -2899,27 +4105,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -2927,40 +4151,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "the case (e.g. patient) that has the property", @@ -2968,25 +4213,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -2997,23 +4254,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3033,7 +4302,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -3044,7 +4316,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3054,55 +4329,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3110,7 +4418,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -3118,15 +4429,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -3134,25 +4454,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -3163,27 +4495,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -3191,40 +4541,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -3236,21 +4607,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -3261,23 +4641,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3332,22 +4724,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3358,46 +4762,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3423,22 +4851,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3449,46 +4889,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3504,7 +4968,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -3515,7 +4982,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3525,40 +4995,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3566,7 +5057,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -3574,15 +5068,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -3590,25 +5093,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -3619,27 +5134,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "The relationship to the disease", @@ -3647,36 +5180,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "A cell line derived from an organismal entity with a disease state that is used as a model of that disease.", @@ -3684,25 +5235,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -3713,23 +5276,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3749,7 +5324,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -3760,7 +5338,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3770,36 +5351,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3807,7 +5406,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -3815,15 +5417,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease or phenotype", @@ -3831,48 +5442,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -3880,32 +5518,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -3913,44 +5566,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3980,22 +5654,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4006,46 +5692,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -4071,22 +5781,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4097,46 +5819,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -4152,7 +5898,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -4163,11 +5912,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "anatomical_context_qualifier": { "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", - "type": "string" + "type": [ + "string", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4177,7 +5932,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", @@ -4185,32 +5943,47 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4218,7 +5991,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -4226,15 +6002,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -4246,24 +6031,36 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -4278,11 +6075,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -4290,19 +6093,31 @@ }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -4310,40 +6125,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -4355,24 +6191,36 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_derivative_qualifier": { "$ref": "#/$defs/ChemicalEntityDerivativeEnum", @@ -4391,11 +6239,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -4404,14 +6258,20 @@ "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -4434,7 +6294,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4448,29 +6311,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4478,50 +6356,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -4537,7 +6442,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -4548,7 +6456,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4558,36 +6469,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4595,7 +6524,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -4603,15 +6535,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -4619,48 +6560,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -4668,32 +6636,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -4701,44 +6684,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -4766,7 +6770,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -4777,7 +6784,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4787,36 +6797,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4824,7 +6852,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -4832,15 +6863,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -4848,21 +6888,30 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -4873,27 +6922,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "the direction is always from regulator to regulated", @@ -4901,32 +6968,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -4934,44 +7016,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5001,22 +7104,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -5024,14 +7139,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5039,43 +7160,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5092,7 +7234,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -5103,11 +7248,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "anatomical_context_qualifier": { "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", - "type": "string" + "type": [ + "string", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5117,36 +7268,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5154,7 +7323,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -5162,15 +7334,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -5178,24 +7359,36 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "object_form_or_variant_qualifier": { "$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum", @@ -5206,11 +7399,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -5218,19 +7417,31 @@ }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -5238,32 +7449,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the chemical entity or entity that is an interactor", @@ -5271,24 +7497,36 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_derivative_qualifier": { "$ref": "#/$defs/ChemicalEntityDerivativeEnum", @@ -5303,11 +7541,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -5316,14 +7560,20 @@ "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5346,7 +7596,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5360,11 +7613,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -5372,21 +7631,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -5398,61 +7666,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5472,7 +7773,10 @@ }, "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -5483,7 +7787,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5493,36 +7800,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5530,7 +7855,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -5538,15 +7866,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease or phenotype", @@ -5554,48 +7891,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -5603,32 +7967,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -5636,44 +8015,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5697,7 +8097,10 @@ }, "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -5708,7 +8111,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5718,36 +8124,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5755,7 +8179,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -5763,15 +8190,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease or phenotype", @@ -5779,48 +8215,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -5828,32 +8291,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -5861,44 +8339,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5942,22 +8441,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -5965,14 +8476,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5980,38 +8497,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -6028,7 +8563,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -6039,7 +8577,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6049,36 +8590,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6086,7 +8645,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -6094,15 +8656,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the chemical element that is the target of the statement", @@ -6110,48 +8681,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -6159,32 +8757,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -6192,44 +8805,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -6249,7 +8883,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -6260,14 +8897,20 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "catalyst_qualifier": { "description": "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical.", "items": { "$ref": "#/$defs/MacromolecularMachineMixin" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6277,36 +8920,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6314,7 +8975,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -6322,15 +8986,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the downstream chemical entity", @@ -6338,48 +9011,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -6387,32 +9087,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the upstream chemical entity", @@ -6420,44 +9135,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -6477,7 +9213,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -6488,7 +9227,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6498,36 +9240,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6535,7 +9295,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -6543,15 +9306,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the disease or phenotype that is affected by the chemical", @@ -6559,48 +9331,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -6608,32 +9407,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -6641,44 +9455,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -6698,7 +9533,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -6709,7 +9547,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6719,36 +9560,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6756,7 +9615,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -6764,15 +9626,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the pathway that is affected by the chemical", @@ -6780,48 +9651,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -6829,32 +9727,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the chemical entity that is affecting the pathway", @@ -6862,44 +9775,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -6930,29 +9864,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6960,44 +9912,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7036,22 +10012,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -7059,14 +10047,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7074,38 +10068,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7132,22 +10144,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -7155,14 +10179,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7170,38 +10200,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7228,22 +10276,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7251,38 +10311,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7308,22 +10386,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7334,46 +10424,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7399,22 +10513,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7422,38 +10548,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7479,22 +10623,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -7502,14 +10658,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7517,38 +10679,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7575,22 +10755,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -7598,14 +10790,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7613,38 +10811,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7671,22 +10887,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7694,38 +10922,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7751,26 +10997,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7781,46 +11042,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7846,22 +11131,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7872,46 +11169,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7938,29 +11259,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7968,44 +11307,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8031,22 +11394,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -8054,14 +11429,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8069,38 +11450,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8120,7 +11519,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -8134,11 +11536,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -8146,21 +11554,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -8172,61 +11589,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8253,29 +11703,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8283,44 +11751,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8347,29 +11839,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8377,44 +11887,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8430,7 +11964,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -8441,7 +11978,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -8451,36 +11991,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8488,7 +12046,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -8496,15 +12057,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "agent helping to realise the given entity (e.g. such as a publication)", @@ -8512,48 +12082,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'", @@ -8561,32 +12158,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "information content entity which an agent has helped realise", @@ -8594,44 +12206,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8651,7 +12284,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -8662,7 +12298,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -8672,55 +12311,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8728,7 +12400,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -8736,15 +12411,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -8752,25 +12436,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -8781,27 +12477,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -8809,40 +12523,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -8854,21 +12589,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -8879,23 +12623,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8926,29 +12682,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8956,44 +12730,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9020,32 +12818,53 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "distribution_download_url": { - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9053,44 +12872,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9117,29 +12960,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9147,50 +13008,80 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "source_logo": { - "type": "string" + "type": [ + "string", + "null" + ] }, "source_web_page": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9217,83 +13108,134 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_dataset": { - "type": "string" + "type": [ + "string", + "null" + ] }, "has_distribution": { - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, "ingest_date": { - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9319,22 +13261,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9342,38 +13296,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9399,22 +13371,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9422,38 +13406,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9490,22 +13492,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9516,46 +13530,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9581,22 +13619,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9607,46 +13657,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9672,22 +13746,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -9695,14 +13781,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9710,43 +13802,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9769,7 +13882,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -9780,7 +13896,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -9790,36 +13909,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9827,7 +13964,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -9835,15 +13975,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "genetic inheritance associated with the specified disease or phenotypic feature.", @@ -9851,48 +14000,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -9900,32 +14076,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "disease or phenotype", @@ -9933,44 +14124,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9990,7 +14202,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -10001,7 +14216,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10011,36 +14229,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10048,7 +14284,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -10056,15 +14295,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "anatomical entity in which the disease or feature is found.", @@ -10072,48 +14320,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -10121,32 +14396,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "disease or phenotype", @@ -10154,44 +14444,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -10211,7 +14522,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -10222,7 +14536,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10232,36 +14549,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10269,7 +14604,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -10277,15 +14615,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -10293,48 +14640,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -10342,32 +14716,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "disease class", @@ -10375,44 +14764,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -10432,7 +14842,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -10443,7 +14856,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10453,55 +14869,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10509,7 +14958,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -10517,15 +14969,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -10533,25 +14994,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -10562,31 +15035,52 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "onset_qualifier": { "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -10594,40 +15088,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "disease class", @@ -10635,25 +15150,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -10664,23 +15191,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -10703,7 +15242,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10717,11 +15259,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -10729,21 +15277,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -10755,61 +15312,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -10855,22 +15445,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -10878,14 +15480,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10893,43 +15501,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -10949,7 +15578,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10964,29 +15596,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -10994,42 +15644,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -11039,31 +15710,46 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -11080,7 +15766,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -11091,7 +15780,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -11101,36 +15793,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11138,7 +15848,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -11146,15 +15859,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -11162,48 +15884,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -11211,32 +15960,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the drug that is an interactor", @@ -11244,44 +16008,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -11311,22 +16096,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -11337,18 +16134,27 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11356,43 +16162,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -11420,7 +16247,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -11431,7 +16261,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -11441,55 +16274,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "$ref": "#/$defs/DruggableGeneCategoryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11497,7 +16363,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -11505,15 +16374,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -11521,25 +16399,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -11550,27 +16440,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -11578,40 +16486,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -11623,21 +16552,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -11648,23 +16586,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -11684,7 +16634,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -11695,7 +16648,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -11705,7 +16661,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "clinical_approval_status": { "$ref": "#/$defs/ClinicalApprovalStatusEnum", @@ -11713,32 +16672,47 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11746,7 +16720,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -11754,18 +16731,27 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "max_research_phase": { "$ref": "#/$defs/ResearchPhaseEnum" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -11773,48 +16759,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -11822,32 +16835,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -11855,44 +16883,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -11912,7 +16961,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -11923,7 +16975,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -11933,7 +16988,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "clinical_approval_status": { "$ref": "#/$defs/ClinicalApprovalStatusEnum", @@ -11941,32 +16999,47 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11974,7 +17047,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -11982,18 +17058,27 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "max_research_phase": { "$ref": "#/$defs/ResearchPhaseEnum" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -12001,48 +17086,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -12050,32 +17162,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -12083,44 +17210,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12150,22 +17298,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -12173,14 +17333,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12188,43 +17354,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12251,22 +17438,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12274,38 +17473,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12324,7 +17541,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -12338,29 +17558,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12368,50 +17603,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12437,22 +17699,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12460,38 +17734,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12523,22 +17815,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12546,38 +17850,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12604,29 +17926,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12634,44 +17974,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12697,22 +18061,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12723,46 +18099,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12778,7 +18178,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -12789,7 +18192,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -12799,36 +18205,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12836,7 +18260,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -12844,15 +18271,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -12860,48 +18296,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -12909,32 +18372,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -12942,44 +18420,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12999,7 +18498,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -13010,7 +18512,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13020,36 +18525,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13057,7 +18580,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -13065,15 +18591,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/Outcome", @@ -13081,52 +18616,82 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "population_context_qualifier": { "description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", - "type": "string" + "type": [ + "string", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -13134,32 +18699,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -13167,49 +18747,73 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "temporal_context_qualifier": { "description": "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -13229,7 +18833,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -13240,7 +18847,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13250,55 +18860,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13306,7 +18949,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -13314,15 +18960,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -13330,25 +18985,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -13359,27 +19026,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -13387,40 +19072,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -13428,25 +19134,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -13457,23 +19175,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -13507,7 +19237,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13521,11 +19254,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -13533,21 +19272,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -13559,61 +19307,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -13632,7 +19413,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13646,29 +19430,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13676,50 +19475,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -13735,7 +19561,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -13746,7 +19575,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13756,36 +19588,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13793,7 +19643,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -13801,15 +19654,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -13817,48 +19679,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -13866,32 +19755,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -13899,44 +19803,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -13966,22 +19891,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13992,46 +19929,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -14057,26 +20018,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14087,50 +20063,77 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "symbol": { "description": "Symbol for a particular thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -14146,7 +20149,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -14157,11 +20163,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "anatomical_context_qualifier": { "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", - "type": "string" + "type": [ + "string", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -14171,7 +20183,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", @@ -14179,32 +20194,47 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14212,7 +20242,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -14220,15 +20253,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -14240,24 +20282,36 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "object_derivative_qualifier": { "$ref": "#/$defs/ChemicalEntityDerivativeEnum", @@ -14276,11 +20330,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -14288,19 +20348,31 @@ }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -14308,40 +20380,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -14353,28 +20446,43 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_derivative_qualifier": { "description": "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier \u2018metabolite\u2019 combines with a \u2018Chemical X\u2019 core concept to express the composed concept \u2018a metabolite of Chemical X\u2019. This qualifier is for the subject of an association (or statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -14389,11 +20497,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -14402,14 +20516,20 @@ "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -14429,7 +20549,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -14440,7 +20563,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -14450,55 +20576,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14506,7 +20665,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -14514,15 +20676,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -14530,25 +20701,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -14559,27 +20742,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "The relationship to the disease", @@ -14587,40 +20788,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -14632,21 +20854,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -14657,23 +20888,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -14703,29 +20946,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14736,46 +20994,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -14791,7 +21073,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -14802,7 +21087,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -14812,55 +21100,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14868,7 +21189,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -14876,15 +21200,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -14892,25 +21225,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -14921,27 +21266,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -14949,40 +21312,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -14994,21 +21378,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15016,30 +21409,45 @@ }, "subject_form_or_variant_qualifier": { "description": "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier \u2018mutation\u2019 combines with the core concept \u2018Gene X\u2019 to express the compose concept \u2018a mutation of Gene X\u2019. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -15134,7 +21542,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -15145,7 +21556,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15155,36 +21569,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15192,7 +21624,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -15200,15 +21635,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -15220,21 +21664,30 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15245,27 +21698,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -15273,14 +21744,20 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", @@ -15288,25 +21765,37 @@ }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -15314,44 +21803,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -15374,7 +21884,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -15385,7 +21898,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15395,55 +21911,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15451,7 +22000,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -15459,15 +22011,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -15475,25 +22036,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15504,27 +22077,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -15532,40 +22123,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -15577,21 +22189,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15602,23 +22223,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -15638,7 +22271,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -15649,7 +22285,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15659,55 +22298,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15715,7 +22387,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -15723,15 +22398,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -15739,25 +22423,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15768,27 +22464,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -15796,40 +22510,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -15841,21 +22576,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15866,23 +22610,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -15902,7 +22658,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -15913,7 +22672,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15923,36 +22685,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15960,7 +22740,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -15968,15 +22751,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "location in which the gene is expressed", @@ -15984,48 +22776,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "expression relationship", @@ -16033,40 +22852,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "quantifier_qualifier": { "description": "can be used to indicate magnitude, or also ranking", - "type": "string" + "type": [ + "string", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "stage_qualifier": { "description": "stage at which the gene is expressed in the site", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16074,44 +22914,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -16131,7 +22992,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16142,7 +23006,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16152,40 +23019,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "expression_site": { "description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16193,7 +23081,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16201,15 +23092,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16217,52 +23117,82 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "phenotypic_state": { "description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -16270,40 +23200,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "quantifier_qualifier": { "description": "Optional quantitative value indicating degree of expression.", - "type": "string" + "type": [ + "string", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "stage_qualifier": { "description": "stage during which gene or protein expression of takes place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16311,44 +23262,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -16368,7 +23340,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16379,7 +23354,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16389,36 +23367,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16426,7 +23422,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16434,15 +23433,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -16450,48 +23458,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "membership of the gene in the given gene family.", @@ -16499,32 +23534,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -16532,44 +23582,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -16589,7 +23660,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16600,7 +23674,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16610,36 +23687,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16647,7 +23742,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16655,15 +23753,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16671,48 +23778,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "homology relationship type", @@ -16720,32 +23854,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16753,44 +23902,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -16810,7 +23980,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16821,7 +23994,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16831,36 +24007,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16868,7 +24062,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16876,15 +24073,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneProductMixin", @@ -16892,48 +24098,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -16941,32 +24174,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -16974,44 +24222,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17031,7 +24300,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -17042,7 +24314,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -17052,36 +24327,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17089,7 +24382,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -17097,15 +24393,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -17113,48 +24418,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -17162,32 +24494,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "gene, product or macromolecular complex that has the function associated with the GO term", @@ -17195,44 +24542,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17252,7 +24620,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -17263,7 +24634,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -17273,36 +24647,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17310,7 +24702,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -17318,15 +24713,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the pathway that includes or is affected by the gene or gene product", @@ -17334,48 +24738,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -17383,32 +24814,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -17416,44 +24862,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17473,7 +24940,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -17484,7 +24954,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -17494,55 +24967,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17550,7 +25056,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -17558,15 +25067,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -17574,25 +25092,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -17603,27 +25133,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -17631,40 +25179,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -17676,21 +25245,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -17701,23 +25279,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17747,22 +25337,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17773,46 +25375,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17838,26 +25464,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17868,46 +25509,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17933,22 +25598,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -17956,25 +25633,37 @@ }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17985,51 +25674,78 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -18046,7 +25762,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -18057,7 +25776,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18067,19 +25789,31 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "end_interbase_coordinate": { "description": "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "genome_build": { "$ref": "#/$defs/StrandEnum", @@ -18090,21 +25824,30 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18112,7 +25855,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -18120,15 +25866,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -18136,48 +25891,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "phase": { "$ref": "#/$defs/PhaseEnum", @@ -18189,36 +25971,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "start_interbase_coordinate": { "description": "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0).", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "strand": { "$ref": "#/$defs/StrandEnum", @@ -18230,44 +26030,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -18297,29 +26118,47 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_zygosity": { - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18330,46 +26169,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -18385,7 +26248,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -18396,7 +26262,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18406,40 +26275,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18447,7 +26337,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -18455,15 +26348,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -18471,25 +26373,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -18500,27 +26414,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "The relationship to the disease", @@ -18528,36 +26460,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "A genotype that has a role in modeling the disease.", @@ -18565,25 +26515,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -18594,23 +26556,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -18630,7 +26604,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -18641,7 +26618,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18651,40 +26631,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18692,7 +26693,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -18700,15 +26704,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "a disease that is associated with that genotype", @@ -18716,25 +26729,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -18745,27 +26770,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "E.g. is pathogenic for", @@ -18773,36 +26816,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "a genotype that is associated in some way with a disease state", @@ -18810,25 +26871,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -18839,23 +26912,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -18875,7 +26960,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -18886,7 +26974,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18896,36 +26987,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18933,7 +27042,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -18941,15 +27053,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "gene implicated in genotype", @@ -18957,48 +27078,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "the relationship type used to connect genotype to gene", @@ -19006,32 +27154,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "parent genotype", @@ -19039,44 +27202,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -19096,7 +27280,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -19107,7 +27294,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19117,36 +27307,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19154,7 +27362,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -19162,15 +27373,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "child genotype", @@ -19178,48 +27398,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -19227,32 +27474,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "parent genotype", @@ -19260,44 +27522,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -19317,7 +27600,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -19328,7 +27614,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19338,55 +27627,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19394,7 +27716,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -19402,15 +27727,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -19418,25 +27752,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -19447,27 +27793,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -19475,40 +27839,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "genotype that is associated with the phenotypic feature", @@ -19516,25 +27901,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -19545,23 +27942,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -19581,7 +27990,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -19592,7 +28004,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19602,36 +28017,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19639,7 +28072,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -19647,15 +28083,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "gene implicated in genotype", @@ -19663,48 +28108,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "the relationship type used to connect genotype to gene", @@ -19712,32 +28184,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "parent genotype", @@ -19745,44 +28232,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -19812,22 +28320,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -19835,14 +28355,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19850,38 +28376,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -19908,22 +28452,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -19931,14 +28487,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19946,43 +28508,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20009,22 +28592,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20032,46 +28627,70 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "latitude": { "description": "latitude", - "type": "number" + "type": [ + "number", + "null" + ] }, "longitude": { "description": "longitude", - "type": "number" + "type": [ + "number", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20097,22 +28716,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20120,51 +28751,78 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "latitude": { "description": "latitude", - "type": "number" + "type": [ + "number", + "null" + ] }, "longitude": { "description": "longitude", - "type": "number" + "type": [ + "number", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20190,22 +28848,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20216,46 +28886,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20281,26 +28975,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20311,46 +29020,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20376,22 +29109,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20399,38 +29144,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20462,22 +29225,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20488,46 +29263,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20553,22 +29352,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20579,46 +29390,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20634,7 +29469,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -20645,7 +29483,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -20655,36 +29496,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20692,7 +29551,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -20700,15 +29562,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -20716,48 +29587,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -20765,32 +29663,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -20798,44 +29711,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20865,22 +29799,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20891,46 +29837,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20949,7 +29919,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -20964,29 +29937,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -20994,50 +29985,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iso_abbreviation": { "description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", - "type": "string" + "type": [ + "string", + "null" + ] }, "issue": { "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -21051,35 +30069,53 @@ "type": "string" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21120,22 +30156,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21146,46 +30194,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21212,29 +30284,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21242,44 +30332,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21315,22 +30429,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21341,46 +30467,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21396,7 +30546,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -21407,7 +30560,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -21417,36 +30573,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21454,7 +30628,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -21462,15 +30639,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -21478,48 +30664,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -21527,32 +30740,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -21560,44 +30788,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21617,7 +30866,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -21628,7 +30880,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -21638,36 +30893,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21675,7 +30948,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -21683,15 +30959,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -21699,48 +30984,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -21748,32 +31060,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -21781,44 +31108,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21838,7 +31186,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -21849,7 +31200,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -21859,36 +31213,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21896,7 +31268,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -21904,15 +31279,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -21920,48 +31304,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -21969,32 +31380,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -22002,44 +31428,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22069,22 +31516,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22095,46 +31554,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22160,22 +31643,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22183,38 +31678,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22230,7 +31743,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -22241,7 +31757,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22251,36 +31770,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22288,7 +31825,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -22296,15 +31836,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.", @@ -22312,48 +31861,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "derivation relationship", @@ -22361,32 +31937,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the material sample being described", @@ -22394,44 +31985,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22451,7 +32063,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -22462,7 +32077,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22472,36 +32090,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22509,7 +32145,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -22517,15 +32156,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease or phenotype", @@ -22533,48 +32181,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -22582,32 +32257,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the material sample being described", @@ -22615,44 +32305,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22682,22 +32393,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22708,46 +32431,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22773,43 +32520,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "The gene product, gene, or complex that catalyzes the reaction", "items": { "$ref": "#/$defs/MacromolecularMachineMixin" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "A chemical entity that is the input for the reaction", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "A chemical entity that is the output for the reaction", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22820,46 +32588,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22875,7 +32667,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -22886,7 +32681,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22896,36 +32694,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22933,7 +32749,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -22941,15 +32760,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -22957,48 +32785,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -23006,32 +32861,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23039,44 +32909,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23096,7 +32987,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -23107,7 +33001,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23117,36 +33014,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23154,7 +33069,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -23162,15 +33080,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23178,48 +33105,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -23227,32 +33181,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23260,44 +33229,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23317,7 +33307,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -23328,7 +33321,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23338,36 +33334,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23375,7 +33389,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -23383,15 +33400,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23399,48 +33425,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -23448,32 +33501,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23481,44 +33549,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23541,7 +33630,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23555,29 +33647,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23585,54 +33692,84 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_metabolite": { "description": "indicates whether a molecular entity is a metabolite", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23651,7 +33788,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23665,11 +33805,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -23677,21 +33823,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -23703,61 +33858,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23789,22 +33977,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23812,38 +34012,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23859,7 +34077,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -23870,7 +34091,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23880,36 +34104,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23917,7 +34159,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -23925,15 +34170,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23941,59 +34195,95 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "population_context_qualifier": { "description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", - "type": "string" + "type": [ + "string", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -24001,32 +34291,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -24034,51 +34339,78 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24108,22 +34440,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24134,46 +34478,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24192,7 +34560,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -24206,33 +34577,51 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24243,62 +34632,98 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_metabolite": { "description": "indicates whether a molecular entity is a metabolite", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24324,22 +34749,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24350,46 +34787,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24415,26 +34876,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24445,46 +34921,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24511,29 +35011,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24541,44 +35059,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24604,22 +35146,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -24627,14 +35181,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24642,38 +35202,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24700,22 +35278,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -24723,14 +35313,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24738,38 +35334,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24796,25 +35410,40 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_taxonomic_rank": { - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24822,38 +35451,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24869,7 +35516,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -24880,11 +35530,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "associated_environmental_context": { "description": "the environment in which the two taxa interact", - "type": "string" + "type": [ + "string", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -24894,36 +35550,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24931,7 +35605,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -24939,15 +35616,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the taxon that is the subject of the association", @@ -24955,48 +35641,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -25004,32 +35717,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the taxon that is the subject of the association", @@ -25037,44 +35765,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -25094,7 +35843,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -25105,7 +35857,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -25115,36 +35870,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25152,7 +35925,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -25160,15 +35936,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the more general taxon", @@ -25176,48 +35961,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -25225,32 +36037,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the more specific taxon", @@ -25258,44 +36085,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -25315,7 +36163,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -25326,7 +36177,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -25336,36 +36190,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25373,7 +36245,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -25381,15 +36256,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "An association between two individual organisms.", @@ -25397,48 +36281,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -25446,32 +36357,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -25479,44 +36405,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -25536,7 +36483,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -25547,7 +36497,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -25557,40 +36510,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25598,7 +36572,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -25606,15 +36583,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -25622,25 +36608,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -25651,27 +36649,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "The relationship to the disease", @@ -25679,36 +36695,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.", @@ -25716,25 +36750,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -25745,23 +36791,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -25781,7 +36839,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -25792,7 +36853,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -25802,36 +36866,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25839,7 +36921,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -25847,15 +36932,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -25863,48 +36957,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "interaction relationship type", @@ -25912,32 +37033,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -25945,44 +37081,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26002,7 +37159,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -26013,7 +37173,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -26023,47 +37186,71 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "identifier for the interaction. This may come from an interaction database such as IMEX.", "type": "string" }, "interacting_molecules_category": { - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -26071,15 +37258,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.", @@ -26087,48 +37283,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "interaction relationship type", @@ -26136,32 +37359,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.", @@ -26169,44 +37407,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26229,7 +37488,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -26244,29 +37506,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -26274,42 +37554,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -26319,31 +37620,46 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26370,22 +37686,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -26393,14 +37721,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26408,43 +37742,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26477,22 +37832,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26503,46 +37870,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26568,43 +37959,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26615,46 +38027,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26680,22 +38116,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -26703,14 +38151,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26718,43 +38172,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26787,43 +38262,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26834,46 +38330,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26909,22 +38429,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26932,38 +38464,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26989,22 +38539,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27015,46 +38577,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27070,7 +38656,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -27081,7 +38670,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -27091,55 +38683,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27147,7 +38772,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -27155,15 +38783,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -27171,25 +38808,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -27200,27 +38849,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -27228,40 +38895,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -27269,25 +38957,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -27298,23 +38998,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27334,7 +39046,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -27345,7 +39060,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -27355,55 +39073,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27411,7 +39162,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -27419,15 +39173,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -27435,25 +39198,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -27464,27 +39239,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -27492,40 +39285,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -27533,25 +39347,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -27562,23 +39388,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27608,22 +39446,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -27631,14 +39481,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27646,38 +39502,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27704,22 +39578,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -27727,14 +39613,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27742,38 +39634,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27800,22 +39710,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27823,38 +39745,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27880,43 +39820,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27927,46 +39888,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27992,22 +39977,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28015,38 +40012,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28072,22 +40087,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28098,46 +40125,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28163,22 +40214,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28189,46 +40252,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28254,22 +40341,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28280,46 +40379,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28335,7 +40458,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -28346,7 +40472,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -28356,36 +40485,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28393,7 +40540,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -28401,15 +40551,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the population that form the object of the association", @@ -28417,48 +40576,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used", @@ -28466,32 +40652,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the population that form the subject of the association", @@ -28499,44 +40700,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28566,22 +40788,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28592,46 +40826,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28647,14 +40905,20 @@ "properties": { "anatomical_context_qualifier": { "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", - "type": "string" + "type": [ + "string", + "null" + ] }, "broad_match": { "description": "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", @@ -28665,29 +40929,47 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "mapped_predicate": { "description": "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs.", - "type": "string" + "type": [ + "string", + "null" + ] }, "narrow_match": { "description": "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "object_derivative_qualifier": { "description": "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier \u2018metabolite\u2019 combines with a \u2018Chemical X\u2019 core concept to express the composed concept \u2018a metabolite of Chemical X\u2019. This qualifier is for the object of an association (or statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -28695,11 +40977,17 @@ }, "object_form_or_variant_qualifier": { "description": "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier \u2018mutation\u2019 combines with the core concept \u2018Gene X\u2019 to express the compose concept \u2018a mutation of Gene X\u2019. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_part_qualifier": { "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -28707,22 +40995,37 @@ }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_derivative_qualifier": { "description": "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier \u2018metabolite\u2019 combines with a \u2018Chemical X\u2019 core concept to express the composed concept \u2018a metabolite of Chemical X\u2019. This qualifier is for the subject of an association (or statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -28730,11 +41033,17 @@ }, "subject_form_or_variant_qualifier": { "description": "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier \u2018mutation\u2019 combines with the core concept \u2018Gene X\u2019 to express the compose concept \u2018a mutation of Gene X\u2019. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_part_qualifier": { "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement).", - "type": "string" + "type": [ + "string", + "null" + ] } }, "required": [ @@ -28752,7 +41061,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -28767,29 +41079,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -28797,42 +41127,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -28842,31 +41193,46 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28893,22 +41259,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28916,38 +41294,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28963,7 +41359,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -28974,7 +41373,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -28984,36 +41386,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29021,7 +41441,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -29029,15 +41452,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -29045,48 +41477,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -29094,32 +41553,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -29127,44 +41601,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29187,7 +41682,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -29201,11 +41699,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -29213,21 +41717,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -29239,61 +41752,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29319,22 +41865,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29345,46 +41903,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29410,29 +41992,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29443,46 +42040,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29508,29 +42129,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29541,46 +42177,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29606,22 +42266,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29632,46 +42304,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29690,7 +42386,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -29705,29 +42404,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -29735,42 +42452,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -29780,31 +42518,46 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29821,11 +42574,17 @@ "properties": { "has_numeric_value": { "description": "connects a quantity value to a number", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_unit": { "description": "connects a quantity value to a unit", - "type": "string" + "type": [ + "string", + "null" + ] } }, "title": "QuantityValue", @@ -29847,22 +42606,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29873,46 +42644,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29938,22 +42733,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29964,46 +42771,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30039,7 +42870,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -30050,7 +42884,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -30060,36 +42897,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30097,7 +42952,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -30105,15 +42963,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -30121,48 +42988,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -30170,25 +43064,37 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "reaction_direction": { "$ref": "#/$defs/ReactionDirectionEnum", @@ -30203,11 +43109,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "stoichiometry": { "description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "subject": { "description": "the chemical entity or entity that is an interactor", @@ -30215,44 +43127,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30272,7 +43205,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -30283,7 +43219,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -30293,36 +43232,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30330,7 +43287,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -30338,15 +43298,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the chemical element that is the target of the statement", @@ -30354,48 +43323,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -30403,25 +43399,37 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "reaction_direction": { "$ref": "#/$defs/ReactionDirectionEnum", @@ -30436,11 +43444,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "stoichiometry": { "description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "subject": { "description": "the chemical entity or entity that is an interactor", @@ -30448,44 +43462,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30515,26 +43550,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30545,46 +43595,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30610,26 +43684,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30640,46 +43729,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30721,29 +43834,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30751,44 +43882,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30839,29 +43994,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30869,21 +44042,33 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "resource_id": { "description": "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.", @@ -30894,31 +44079,46 @@ "description": "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "upstream_resource_ids": { "description": "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.", - "type": "string" + "type": [ + "string", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30936,7 +44136,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -30947,7 +44150,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -30957,36 +44163,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30994,7 +44218,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -31002,15 +44229,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -31018,48 +44254,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -31067,32 +44330,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -31100,44 +44378,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31166,7 +44465,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -31177,7 +44479,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -31187,36 +44492,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31224,7 +44547,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -31232,15 +44558,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -31248,48 +44583,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -31297,32 +44659,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -31330,44 +44707,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31397,33 +44795,51 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "The state of the sequence w.r.t a reference sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_gene": { "description": "Each allele can be associated with any number of genes", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31434,46 +44850,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31492,7 +44932,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -31507,29 +44950,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Serials (journals) should have industry-standard identifier such as from ISSN.", @@ -31537,50 +44998,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iso_abbreviation": { "description": "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.", - "type": "string" + "type": [ + "string", + "null" + ] }, "issue": { "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -31590,36 +45078,54 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "description": "Should generally be set to an ontology class defined term for 'serial' or 'journal'.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31646,22 +45152,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -31669,14 +45187,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31684,38 +45208,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31742,22 +45284,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31768,46 +45322,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31826,7 +45404,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -31840,29 +45421,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31870,54 +45466,84 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_metabolite": { "description": "indicates whether a molecular entity is a metabolite", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31943,33 +45569,51 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "The state of the sequence w.r.t a reference sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_gene": { "description": "Each allele can be associated with any number of genes", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31980,46 +45624,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32045,22 +45713,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -32068,14 +45748,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32083,38 +45769,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32141,15 +45845,24 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", @@ -32164,14 +45877,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32179,43 +45898,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32260,22 +46000,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32283,38 +46035,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32340,22 +46110,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32366,46 +46148,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32432,29 +46238,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32462,44 +46286,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32515,7 +46363,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -32526,7 +46377,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -32536,36 +46390,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32573,7 +46445,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -32581,15 +46456,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "An association between individuals of different taxa.", @@ -32597,48 +46481,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -32646,32 +46557,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -32679,44 +46605,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32762,29 +46709,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32792,44 +46757,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32855,22 +46844,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32881,46 +46882,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32936,7 +46961,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -32947,7 +46975,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -32957,36 +46988,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32994,7 +47043,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -33002,15 +47054,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -33018,48 +47079,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -33067,32 +47155,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -33100,44 +47203,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -33167,26 +47291,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33197,46 +47336,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -33262,43 +47425,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_device": { "description": "connects an entity to one or more (medical) devices", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_drug": { "description": "connects an entity to one or more drugs", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_procedure": { "description": "connects an entity to one or more (medical) procedures", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33306,43 +47490,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -33358,7 +47563,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -33369,7 +47577,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -33379,40 +47590,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33420,7 +47652,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -33428,15 +47663,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -33444,25 +47688,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -33473,27 +47729,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "The relationship to the disease", @@ -33501,36 +47775,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "A variant that has a role in modeling the disease.", @@ -33538,25 +47830,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -33567,23 +47871,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -33603,7 +47919,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -33614,7 +47933,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -33624,40 +47946,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33665,7 +48008,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -33673,15 +48019,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "a disease that is associated with that variant", @@ -33689,25 +48044,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -33718,27 +48085,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "E.g. is pathogenic for", @@ -33746,36 +48131,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "a sequence variant in which the allele state is associated in some way with the disease state", @@ -33783,25 +48186,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -33812,23 +48227,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -33848,7 +48275,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -33859,7 +48289,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -33869,36 +48302,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33906,7 +48357,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -33914,15 +48368,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -33930,48 +48393,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -33979,32 +48469,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "a sequence variant in which the allele state is associated with some other entity", @@ -34012,44 +48517,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34069,7 +48595,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -34080,7 +48609,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -34090,40 +48622,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "expression_site": { "description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34131,7 +48684,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -34139,15 +48695,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -34155,52 +48720,82 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "phenotypic_state": { "description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -34208,40 +48803,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "quantifier_qualifier": { "description": "Optional quantitative value indicating degree of expression.", - "type": "string" + "type": [ + "string", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "stage_qualifier": { "description": "stage during which gene or protein expression of takes place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "a sequence variant in which the allele state is associated with some other entity", @@ -34249,44 +48865,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34306,7 +48943,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -34317,7 +48957,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -34327,55 +48970,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34383,7 +49059,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -34391,15 +49070,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -34407,25 +49095,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -34436,27 +49136,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -34464,40 +49182,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "a sequence variant in which the allele state is associated in some way with the phenotype state", @@ -34505,25 +49244,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -34534,23 +49285,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34570,7 +49333,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -34581,7 +49347,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -34591,56 +49360,89 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number in object population that carry a particular allele, aka allele count", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { "description": "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "number all populations that carry a particular allele, aka allele number", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34648,7 +49450,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -34656,15 +49461,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the population that is observed to have the frequency", @@ -34672,48 +49486,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -34721,32 +49562,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "an allele that has a certain frequency in a given population", @@ -34754,44 +49610,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34821,22 +49698,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34847,46 +49736,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34912,22 +49825,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34938,46 +49863,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34996,7 +49945,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -35011,29 +49963,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -35041,42 +50011,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -35086,31 +50077,46 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -35137,22 +50143,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -35160,14 +50178,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -35175,38 +50199,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ diff --git a/project/owl/biolink_model.owl.ttl b/project/owl/biolink_model.owl.ttl index 17413a657..ae6f21d6d 100644 --- a/project/owl/biolink_model.owl.ttl +++ b/project/owl/biolink_model.owl.ttl @@ -123,10 +123,10 @@ biolink:HospitalizationOutcome a owl:Class ; biolink:MappingCollection a owl:Class ; rdfs:label "mapping collection" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:PredicateMapping ; owl:onProperty biolink:predicate_mappings ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PredicateMapping ; + owl:minCardinality 0 ; owl:onProperty biolink:predicate_mappings ], linkml:ClassDefinition ; skos:definition "A collection of deprecated mappings." ; @@ -2593,16 +2593,16 @@ biolink:AccessibleDnaRegion a owl:Class ; rdfs:label "accessible dna region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], biolink:RegulatoryRegion ; skos:altLabel "atac-seq accessible region", "dnase-seq accessible region" ; @@ -2648,29 +2648,29 @@ biolink:AccessibleDnaRegion a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], @@ -2681,32 +2681,32 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; skos:inScheme . @@ -2799,6 +2799,9 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BehavioralFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Behavior ; owl:onProperty biolink:subject ], @@ -2806,17 +2809,14 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BehavioralFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; skos:inScheme . @@ -2844,20 +2844,20 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], biolink:Publication ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; skos:inScheme . @@ -2883,10 +2883,10 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; biolink:CausalGeneToDiseaseAssociation a owl:Class ; rdfs:label "causal gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -2895,17 +2895,17 @@ biolink:CausalGeneToDiseaseAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -2998,8 +2998,8 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], @@ -3007,11 +3007,11 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:allValuesFrom biolink:CellLine ; + owl:onProperty biolink:subject ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; skos:inScheme . @@ -3024,167 +3024,167 @@ biolink:CellLineToEntityAssociationMixin a owl:Class ; biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; skos:inScheme . @@ -3192,23 +3192,17 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], @@ -3216,7 +3210,13 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . @@ -3224,38 +3224,38 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -3266,107 +3266,107 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], biolink:Association ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; skos:exactMatch SIO:001257 ; @@ -3375,7 +3375,10 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment side effect disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -3384,10 +3387,7 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; @@ -3416,20 +3416,20 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:catalyst_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], @@ -3437,16 +3437,16 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:minCardinality 0 ; + owl:onProperty biolink:catalyst_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:ChemicalToChemicalAssociation ; skos:definition "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; @@ -3457,17 +3457,17 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; @@ -3477,25 +3477,25 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalToPathwayAssociation a owl:Class ; rdfs:label "chemical to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Pathway ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a chemical entity and a biological process or pathway." ; @@ -3546,10 +3546,10 @@ biolink:ClinicalMeasurement a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute_type ], biolink:ClinicalAttribute ; skos:definition "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; @@ -3612,29 +3612,26 @@ biolink:ConfidenceLevel a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; owl:allValuesFrom biolink:Agent ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationContentEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -3642,8 +3639,11 @@ biolink:ContributorAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:InformationContentEntity ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:qualifiers ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; skos:inScheme . @@ -3651,28 +3651,28 @@ biolink:ContributorAssociation a owl:Class ; biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ; rdfs:label "correlated gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3691,10 +3691,10 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; rdfs:label "disease or phenotypic feature exposure" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:PathologicalEntityMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin ], + owl:someValuesFrom biolink:ExposureEvent ], biolink:Attribute ; skos:definition "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; skos:inScheme . @@ -3702,16 +3702,19 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneticInheritance ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneticInheritance ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -3719,9 +3722,6 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; skos:inScheme . @@ -3729,17 +3729,17 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to location association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; skos:inScheme . @@ -3748,10 +3748,10 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; rdfs:label "disease to exposure event association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin ], + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin ], biolink:Association ; skos:definition "An association between an exposure event and a disease." ; skos:inScheme . @@ -3759,41 +3759,41 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Onset ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:onset_qualifier ], + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:closeMatch dcid:DiseaseSymptomAssociation ; skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; @@ -3845,8 +3845,8 @@ biolink:DrugToEntityAssociationMixin a owl:Class ; biolink:DrugToGeneAssociation a owl:Class ; rdfs:label "drug to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DrugToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -3854,8 +3854,8 @@ biolink:DrugToGeneAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a drug and a gene or gene product." ; skos:inScheme ; @@ -3893,13 +3893,19 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -3911,40 +3917,34 @@ biolink:DruggableGeneToDiseaseAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:EntityToDiseaseAssociation a owl:Class ; rdfs:label "entity to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:allValuesFrom biolink:ResearchPhaseEnum ; owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:max_research_phase ], biolink:Association ; skos:inScheme . @@ -3963,10 +3963,13 @@ biolink:EntityToOutcomeAssociationMixin a owl:Class ; biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "entity to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ResearchPhaseEnum ; + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ResearchPhaseEnum ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -3975,11 +3978,8 @@ biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; - owl:onProperty biolink:clinical_approval_status ], biolink:Association ; skos:inScheme . @@ -4020,23 +4020,23 @@ biolink:Event a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Transcript ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Exon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" ; skos:inScheme . @@ -4044,26 +4044,26 @@ biolink:ExonToTranscriptRelationship a owl:Class ; biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:time ; owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:temporal_context_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:population_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], biolink:Association ; skos:definition "An association between an exposure event and an outcome." ; skos:inScheme . @@ -4071,6 +4071,9 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; @@ -4079,9 +4082,6 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:ExposureEvent ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; skos:inScheme . @@ -4139,175 +4139,175 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; rdfs:label "gene affects chemical association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], biolink:Association ; skos:definition "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; skos:inScheme . @@ -4315,17 +4315,17 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "gene as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -4336,39 +4336,39 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -4656,68 +4656,68 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; biolink:GeneRegulatesGeneAssociation a owl:Class ; rdfs:label "gene regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme . @@ -4727,48 +4727,48 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:quantifier_qualifier ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; @@ -4778,17 +4778,17 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneExpressionMixin ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; skos:inScheme . @@ -4797,31 +4797,31 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; rdfs:label "gene to gene family association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneFamily ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneFamily ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; skos:inScheme . @@ -4829,17 +4829,23 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -4849,12 +4855,6 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], biolink:GeneToGeneAssociation ; skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; skos:inScheme . @@ -4862,13 +4862,10 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:GeneProductMixin ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneProductMixin ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -4876,18 +4873,21 @@ biolink:GeneToGeneProductRelationship a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" ; skos:inScheme . @@ -4895,10 +4895,10 @@ biolink:GeneToGeneProductRelationship a owl:Class ; biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -4907,10 +4907,10 @@ biolink:GeneToGoTermAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; @@ -4920,26 +4920,26 @@ biolink:GeneToGoTermAssociation a owl:Class ; biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." ; skos:inScheme . @@ -4947,29 +4947,29 @@ biolink:GeneToPathwayAssociation a owl:Class ; biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:exactMatch WBVocab:Gene-Phenotype-Association ; skos:inScheme . @@ -4978,13 +4978,13 @@ biolink:Genome a owl:Class ; rdfs:label "genome" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:closeMatch dcid:GenomeAssemblyUnit ; skos:definition "A genome is the sum of genetic material within a cell or virion." ; @@ -4997,22 +4997,22 @@ biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], + owl:someValuesFrom biolink:OntologyClass ], biolink:Attribute ; skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; skos:inScheme . @@ -5020,17 +5020,17 @@ biolink:GenomicBackgroundExposure a owl:Class ; biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "genotype as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], @@ -5041,30 +5041,30 @@ biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; @@ -5073,32 +5073,32 @@ biolink:GenotypeToGeneAssociation a owl:Class ; biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" ; skos:inScheme . @@ -5109,26 +5109,26 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; skos:inScheme . @@ -5136,11 +5136,8 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], @@ -5151,16 +5148,19 @@ biolink:GenotypeToVariantAssociation a owl:Class ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." ; @@ -5200,13 +5200,13 @@ biolink:GeographicExposure a owl:Class ; biolink:GeographicLocationAtTime a owl:Class ; rdfs:label "geographic location at time" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; + owl:maxCardinality 1 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:time ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:timepoint ], biolink:GeographicLocation ; skos:definition "a location that can be described in lat/long coordinates, for a particular time" ; @@ -5227,14 +5227,14 @@ biolink:GrossAnatomicalStructure a owl:Class ; biolink:Haplotype a owl:Class ; rdfs:label "haplotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:definition "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; skos:exactMatch , @@ -5265,32 +5265,32 @@ biolink:Human a owl:Class ; biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:label "information content entity to named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; skos:inScheme . @@ -5369,7 +5369,7 @@ biolink:MacromolecularComplex a owl:Class ; biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; rdfs:label "macromolecular machine to biological process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -5378,7 +5378,7 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcess ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; @@ -5387,11 +5387,11 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; rdfs:label "macromolecular machine to cellular component association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], - [ a owl:Restriction ; owl:allValuesFrom biolink:CellularComponent ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -5408,10 +5408,10 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; @@ -5423,32 +5423,32 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:MaterialSample ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." ; skos:inScheme . @@ -5457,10 +5457,10 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "material sample to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between a material sample and a disease or phenotype." ; skos:inScheme . @@ -5482,22 +5482,22 @@ biolink:MicroRNA a owl:Class ; biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; @@ -5506,8 +5506,8 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], @@ -5518,11 +5518,11 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; skos:inScheme . @@ -5530,20 +5530,20 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -5551,10 +5551,10 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; @@ -5563,38 +5563,47 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:population_context_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:population_context_qualifier ], @@ -5602,38 +5611,29 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_context_qualifier ], biolink:Association ; skos:inScheme . @@ -5648,13 +5648,13 @@ biolink:NucleosomeModification a owl:Class ; rdfs:label "nucleosome modification" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:EpigenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity ], + owl:someValuesFrom biolink:GeneProductIsoformMixin ], biolink:BiologicalEntity ; skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; skos:inScheme . @@ -5670,33 +5670,33 @@ biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme . @@ -5704,37 +5704,37 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:associated_environmental_context ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], @@ -5748,14 +5748,17 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -5764,13 +5767,10 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; skos:inScheme . @@ -5778,22 +5778,22 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:label "organism to organism association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:IndividualOrganism ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:IndividualOrganism ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . @@ -5802,69 +5802,69 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:allValuesFrom biolink:OrganismalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], biolink:Association ; skos:inScheme . biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:interacting_molecules_category ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:interacting_molecules_category ], + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:interacting_molecules_category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:id ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; skos:inScheme . @@ -5956,31 +5956,31 @@ biolink:Phenomenon a owl:Class ; biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ; rdfs:label "phenotypic feature to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], - biolink:Association ; - skos:inScheme . - -biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a owl:Class ; + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + biolink:Association ; + skos:inScheme . + +biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "phenotypic feature to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; skos:inScheme . @@ -6027,31 +6027,31 @@ biolink:Plant a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "An association between a two populations" ; @@ -6069,194 +6069,194 @@ biolink:PosttranslationalModification a owl:Class ; biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:mapped_predicate ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:mapped_predicate ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:exact_match ], + owl:maxCardinality 1 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:broad_match ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_part_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:narrow_match ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:narrow_match ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:mapped_predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], linkml:ClassDefinition ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; skos:inScheme . @@ -6275,19 +6275,13 @@ biolink:ProcessRegulatesProcessAssociation a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; @@ -6295,6 +6289,12 @@ biolink:ProcessRegulatesProcessAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], @@ -6328,10 +6328,10 @@ biolink:ProteinFamily a owl:Class ; rdfs:label "protein family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:BiologicalEntity ; skos:exactMatch , WIKIDATA:Q2278983 ; @@ -6392,28 +6392,28 @@ biolink:RNAProductIsoform a owl:Class ; biolink:ReactionToCatalystAssociation a owl:Class ; rdfs:label "reaction to catalyst association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:ReactionToParticipantAssociation ; skos:inScheme . biolink:ReagentTargetedGene a owl:Class ; rdfs:label "reagent targeted gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:altLabel "sequence targeting reagent" ; skos:definition "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; @@ -6490,23 +6490,23 @@ biolink:SequenceEnum a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Treatment ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:inScheme ; @@ -6515,47 +6515,47 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:issue ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:issue ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], biolink:Publication ; skos:altLabel "journal" ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; @@ -6653,19 +6653,19 @@ biolink:StudyVariable a owl:Class ; biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; @@ -6689,22 +6689,22 @@ biolink:TextMiningResult a owl:Class ; biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Transcript ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is a collection of transcripts" ; @@ -6714,16 +6714,16 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; rdfs:label "transcription factor binding site" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GenomicEntity ], biolink:RegulatoryRegion ; skos:altLabel "binding site", "tf binding site" ; @@ -6734,20 +6734,20 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "variant as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:VariantToDiseaseAssociation ; skos:inScheme . @@ -6772,11 +6772,8 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], @@ -6784,67 +6781,70 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], biolink:Association ; skos:inScheme . biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_count ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_total ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQualifierMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_quotient ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], biolink:Association ; skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" ; skos:inScheme . @@ -7424,40 +7424,40 @@ biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:iso_abbreviation ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], + owl:maxCardinality 1 ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:issue ], + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], biolink:Publication ; skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; skos:exactMatch fabio:article, @@ -7490,32 +7490,32 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:chapter ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:published_in ], + owl:maxCardinality 1 ; + owl:onProperty biolink:chapter ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:published_in ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:chapter ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:published_in ], biolink:Publication ; skos:inScheme . @@ -7533,8 +7533,8 @@ biolink:Case a owl:Class ; biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "cell line to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -7542,8 +7542,8 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], @@ -7585,26 +7585,26 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:C rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:FDA_adverse_event_level ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; + owl:onProperty biolink:FDA_adverse_event_level ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:FDA_adverse_event_level ], biolink:Association ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; @@ -7722,10 +7722,10 @@ biolink:GeneFamily a owl:Class ; rdfs:label "gene family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; skos:altLabel "orthogroup", "protein family" ; @@ -7740,38 +7740,23 @@ biolink:GeneFamily a owl:Class ; biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:start_interbase_coordinate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:phase ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:genome_build ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:StrandEnum ; - owl:onProperty biolink:genome_build ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhaseEnum ; - owl:onProperty biolink:phase ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:end_interbase_coordinate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -7779,38 +7764,53 @@ biolink:GenomicSequenceLocalization a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:StrandEnum ; + owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:StrandEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:end_interbase_coordinate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:phase ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:PhaseEnum ; + owl:onProperty biolink:phase ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:strand ], + owl:onProperty biolink:genome_build ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:StrandEnum ; + owl:onProperty biolink:genome_build ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -7820,38 +7820,38 @@ biolink:GenomicSequenceLocalization a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -7865,22 +7865,22 @@ biolink:GeographicLocation a owl:Class ; rdfs:label "geographic location" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:longitude ], + owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:longitude ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:longitude ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:latitude ], + owl:onProperty biolink:longitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch STY:T083, @@ -7925,10 +7925,10 @@ biolink:PairwiseGeneToGeneInteraction a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; @@ -7962,11 +7962,14 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:reaction_direction ], + owl:allValuesFrom biolink:ReactionSideEnum ; + owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -7975,27 +7978,24 @@ biolink:ReactionToParticipantAssociation a owl:Class ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stoichiometry ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:stoichiometry ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ReactionSideEnum ; owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:reaction_side ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; owl:allValuesFrom xsd:integer ; owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:stoichiometry ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:stoichiometry ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:reaction_direction ], biolink:ChemicalToChemicalAssociation ; skos:inScheme . @@ -8034,23 +8034,23 @@ biolink:Treatment a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:has_drug ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Device ; + owl:minCardinality 0 ; owl:onProperty biolink:has_device ], [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:has_procedure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Device ; owl:onProperty biolink:has_device ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_procedure ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], biolink:NamedThing ; skos:altLabel "medical action", "medical intervention" ; @@ -8063,38 +8063,38 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -8102,7 +8102,10 @@ biolink:VariantToDiseaseAssociation a owl:Class ; biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -8111,16 +8114,13 @@ biolink:VariantToGeneAssociation a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; @@ -8779,20 +8779,20 @@ biolink:ActivityAndBehavior a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], @@ -8827,23 +8827,14 @@ biolink:ChemicalRole a owl:Class ; biolink:ChemicalToChemicalAssociation a owl:Class ; rdfs:label "chemical to chemical association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -8851,11 +8842,20 @@ biolink:ChemicalToChemicalAssociation a owl:Class ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; skos:inScheme . @@ -8932,56 +8932,56 @@ biolink:FrequencyQualifierMixin a owl:Class ; biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme ; skos:narrowMatch WBVocab:Gene-Phenotype-Association, @@ -9037,25 +9037,25 @@ biolink:Onset a owl:Class ; biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "A relationship between two organism taxon nodes" ; @@ -9104,16 +9104,16 @@ biolink:RegulatoryRegion a owl:Class ; rdfs:label "regulatory region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:altLabel "regulatory element" ; skos:definition "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; @@ -9464,10 +9464,10 @@ biolink:CellularComponent a owl:Class ; biolink:DatasetDistribution a owl:Class ; rdfs:label "dataset distribution" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; @@ -9480,23 +9480,23 @@ biolink:DatasetDistribution a owl:Class ; biolink:DatasetSummary a owl:Class ; rdfs:label "dataset summary" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:source_web_page ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:source_web_page ], + owl:onProperty biolink:source_logo ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:source_logo ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:source_logo ], + owl:onProperty biolink:source_web_page ], biolink:InformationContentEntity ; skos:definition "an item that holds summary level information about a dataset." ; skos:inScheme . @@ -9526,20 +9526,20 @@ biolink:GeneToGeneAssociation a owl:Class ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:altLabel "molecular or genetic interaction" ; skos:definition "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; @@ -9621,23 +9621,23 @@ biolink:Protein a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom ; + owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_unit ], [ a owl:Restriction ; - owl:allValuesFrom ; + owl:minCardinality 0 ; owl:onProperty biolink:has_unit ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_numeric_value ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_unit ], + owl:onProperty biolink:has_numeric_value ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; skos:inScheme . @@ -9652,23 +9652,23 @@ biolink:ResourceRoleEnum a owl:Class ; biolink:SequenceFeatureRelationship a owl:Class ; rdfs:label "sequence feature relationship" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:object ], biolink:Association ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; skos:exactMatch CHADO:feature_relationship ; @@ -9789,32 +9789,32 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:ingest_date ], - [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_distribution ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_distribution ], + owl:onProperty biolink:has_dataset ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:allValuesFrom biolink:Dataset ; owl:onProperty biolink:has_dataset ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_dataset ], + owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:ingest_date ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; owl:allValuesFrom biolink:DatasetDistribution ; owl:onProperty biolink:has_distribution ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_dataset ], biolink:InformationContentEntity ; skos:definition "an item that holds version level information about a dataset." ; skos:inScheme . @@ -9843,13 +9843,16 @@ biolink:FDAIDAAdverseEventEnum a owl:Class ; biolink:FunctionalAssociation a owl:Class ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -9857,9 +9860,6 @@ biolink:FunctionalAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; skos:inScheme . @@ -10247,38 +10247,38 @@ biolink:CellularOrganism a owl:Class ; biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ApprovalStatusEnum ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ApprovalStatusEnum ; - owl:onProperty biolink:highest_FDA_approval_status ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:routes_of_delivery ], + owl:maxCardinality 1 ; + owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:allValuesFrom biolink:DrugDeliveryEnum ; owl:onProperty biolink:routes_of_delivery ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ApprovalStatusEnum ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:highest_FDA_approval_status ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:routes_of_delivery ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ApprovalStatusEnum ; + owl:onProperty biolink:highest_FDA_approval_status ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -10304,20 +10304,20 @@ biolink:GeneProductMixin a owl:Class ; biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], @@ -10325,8 +10325,8 @@ biolink:GeneToDiseaseAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:closeMatch dcid:DiseaseGeneAssociation ; skos:exactMatch SIO:000983 ; @@ -10342,38 +10342,38 @@ biolink:MacromolecularMachineMixin a owl:Class ; biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:maxCardinality 1 ; owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; + owl:minCardinality 0 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:Occurrent ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_output ], biolink:BiologicalProcessOrActivity ; skos:altLabel "molecular event", "molecular function", @@ -10393,38 +10393,38 @@ biolink:PhysicalEssenceOrOccurrent a owl:Class ; biolink:RetrievalSource a owl:Class ; rdfs:label "retrieval source" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 0 ; owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:resource_id ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; owl:allValuesFrom biolink:ResourceRoleEnum ; owl:onProperty biolink:resource_role ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:upstream_resource_ids ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:resource_id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:upstream_resource_ids ], + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:resource_role ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:resource_id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], biolink:InformationContentEntity ; skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; skos:inScheme . @@ -10768,10 +10768,10 @@ biolink:Drug a owl:Class ; rdfs:label "drug" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:OntologyClass ], biolink:MolecularMixture ; skos:broadMatch STY:T121 ; skos:definition "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; @@ -10789,20 +10789,20 @@ biolink:Genotype a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Zygosity ; - owl:onProperty biolink:has_zygosity ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:allValuesFrom biolink:Zygosity ; + owl:onProperty biolink:has_zygosity ], biolink:BiologicalEntity ; skos:definition "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; skos:exactMatch , @@ -10896,67 +10896,67 @@ biolink:AgentTypeEnum a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:deprecated ], + owl:allValuesFrom biolink:Attribute ; + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:maxCardinality 1 ; + owl:onProperty biolink:description ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Attribute ; - owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_attribute ], + owl:maxCardinality 1 ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:description ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:category ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:description ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:description ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:deprecated ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:deprecated ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iri ], + owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:deprecated ], linkml:ClassDefinition ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; @@ -11038,16 +11038,16 @@ biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], + owl:someValuesFrom biolink:GenomicEntity ], biolink:MolecularEntity ; skos:altLabel "genomic entity", "sequence feature" ; @@ -11178,32 +11178,32 @@ biolink:BiologicalProcessOrActivity a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:allValuesFrom biolink:PhysicalEntity ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:has_input ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_output ], @@ -11215,37 +11215,37 @@ biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:address ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:affiliation ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:address ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:address ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:affiliation ], + owl:onProperty biolink:name ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -11361,14 +11361,14 @@ biolink:DirectionQualifierEnum a owl:Class ; biolink:MolecularEntity a owl:Class ; rdfs:label "molecular entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:is_metabolite ], - [ a owl:Restriction ; owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:is_metabolite ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:is_metabolite ], biolink:ChemicalEntity ; skos:definition "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; skos:inScheme ; @@ -11380,13 +11380,13 @@ biolink:MolecularEntity a owl:Class ; biolink:OrganismTaxon a owl:Class ; rdfs:label "organism taxon" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:TaxonomicRank ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:TaxonomicRank ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:has_taxonomic_rank ], biolink:NamedThing ; skos:altLabel "taxon", @@ -11418,40 +11418,40 @@ biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:license ], + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:allValuesFrom xsd:date ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:format ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:license ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:rights ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:rights ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:format ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:rights ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:license ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:creation_date ], + owl:onProperty biolink:format ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:format ], + owl:onProperty biolink:creation_date ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:rights ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:rights ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:license ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -11510,15 +11510,6 @@ biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -11527,32 +11518,41 @@ biolink:Attribute a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_attribute_type ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:has_qualitative_value ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 0 ; owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iri ], + owl:onProperty biolink:name ], biolink:NamedThing ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; skos:exactMatch SIO:000614 ; @@ -11577,35 +11577,35 @@ biolink:object_direction_qualifier a owl:ObjectProperty ; biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:symbol ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:symbol ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneOrGeneProduct ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:minCardinality 0 ; + owl:onProperty biolink:symbol ], biolink:BiologicalEntity ; skos:broadMatch ; skos:definition "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; @@ -11619,38 +11619,38 @@ biolink:Gene a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene ], biolink:BiologicalEntity ; skos:altLabel "allele" ; skos:closeMatch , @@ -11694,68 +11694,68 @@ biolink:AnatomicalEntity a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:minCardinality 1 ; + owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:summary ], + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:mesh_terms ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:authors ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:keywords ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:pages ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:summary ], + owl:onProperty biolink:keywords ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:pages ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:keywords ], + owl:onProperty biolink:authors ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:publication_type ], + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:pages ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:keywords ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:mesh_terms ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:authors ], + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:publication_type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:mesh_terms ], biolink:InformationContentEntity ; skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; skos:exactMatch IAO:0000311 ; @@ -11779,56 +11779,56 @@ biolink:BiologicalEntity a owl:Class ; biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:trade_name ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:trade_name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:available_from ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:max_tolerated_dose ], + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:is_toxic ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:is_toxic ], + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalRole ; owl:onProperty biolink:has_chemical_role ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:available_from ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:trade_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:max_tolerated_dose ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty biolink:available_from ], biolink:NamedThing ; skos:broadMatch STY:T167 ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; @@ -11967,260 +11967,260 @@ biolink:association_slot a owl:DatatypeProperty ; biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_predicate ], + owl:onProperty biolink:p_value ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_source ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:publications ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:p_value ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:p_value ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:knowledge_source ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_closure ], + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; + owl:minCardinality 0 ; owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_category ], + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_object ], + owl:allValuesFrom biolink:AgentTypeEnum ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_label_closure ], + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_category_closure ], + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:timepoint ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:negated ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_label_closure ], + owl:allValuesFrom biolink:Study ; + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AgentTypeEnum ; - owl:onProperty biolink:agent_type ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object_category_closure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_closure ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category_closure ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:float ; owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:KnowledgeLevelEnum ; - owl:onProperty biolink:knowledge_level ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:agent_type ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_supporting_studies ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_subject ], + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:KnowledgeLevelEnum ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:retrieval_source_ids ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:p_value ], + owl:minCardinality 0 ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:adjusted_p_value ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_category ], + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_category ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:knowledge_source ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_label_closure ], + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_namespace ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_closure ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; - owl:onProperty biolink:adjusted_p_value ], + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_category_closure ], + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:negated ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:original_object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_closure ], + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Study ; - owl:onProperty biolink:has_supporting_studies ], + owl:minCardinality 0 ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_category_closure ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:knowledge_source ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -12240,38 +12240,38 @@ biolink:related_to_at_instance_level a owl:DatatypeProperty, biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:full_name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:full_name ], + owl:onProperty biolink:synonym ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:provided_by ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], + owl:minCardinality 1 ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:full_name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:full_name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:provided_by ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:provided_by ], + owl:onProperty biolink:category ], biolink:Entity ; skos:definition "a databased entity or concept/class" ; skos:exactMatch STY:T071, @@ -12324,891 +12324,678 @@ biolink:subject a owl:ObjectProperty ; skos:inScheme . [] a owl:Restriction ; - rdfs:subClassOf biolink:WebPage ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:WebPage . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Book ; + rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Book . + owl:someValuesFrom biolink:PathologicalAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicSequenceLocalization ; + rdfs:subClassOf biolink:NucleosomeModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicSequenceLocalization . + owl:someValuesFrom biolink:NucleosomeModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinFamily ; + rdfs:subClassOf biolink:EnvironmentalFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinFamily . + owl:someValuesFrom biolink:EnvironmentalFeature . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Phenomenon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Phenomenon . [] a owl:Restriction ; - rdfs:subClassOf biolink:LifeStage ; + rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LifeStage . + owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicQuality ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicQuality . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Hospitalization ; + rdfs:subClassOf biolink:Procedure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Hospitalization . + owl:someValuesFrom biolink:Procedure . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceAssociation ; + rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceAssociation . + owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalProcess ; + rdfs:subClassOf biolink:Vertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalProcess . + owl:someValuesFrom biolink:Vertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:Drug ; + rdfs:subClassOf biolink:DatasetVersion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Drug . + owl:someValuesFrom biolink:DatasetVersion . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicExposure ; + rdfs:subClassOf biolink:Pathway ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicExposure . + owl:someValuesFrom biolink:Pathway . [] a owl:Restriction ; - rdfs:subClassOf biolink:TextMiningResult ; + rdfs:subClassOf biolink:ComplexChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TextMiningResult . + owl:someValuesFrom biolink:ComplexChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalTrial ; + rdfs:subClassOf biolink:Haplotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalTrial . + owl:someValuesFrom biolink:Haplotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToCatalystAssociation . + owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocationAtTime ; + rdfs:subClassOf biolink:JournalArticle ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocationAtTime . + owl:someValuesFrom biolink:JournalArticle . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; + rdfs:subClassOf biolink:StudyPopulation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . + owl:someValuesFrom biolink:StudyPopulation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; + rdfs:subClassOf biolink:GenomicBackgroundExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceFeatureRelationship . + owl:someValuesFrom biolink:GenomicBackgroundExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:SequenceVariant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:SequenceVariant . [] a owl:Restriction ; - rdfs:subClassOf biolink:Entity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Entity . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SensitivityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; + rdfs:subClassOf biolink:GeographicLocation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . + owl:someValuesFrom biolink:GeographicLocation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariant ; + rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariant . + owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SpecificityQuantifier . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivity . + owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxon ; + rdfs:subClassOf biolink:Transcript ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxon . + owl:someValuesFrom biolink:Transcript . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:sex_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Behavior ; + rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Behavior . + owl:someValuesFrom biolink:ChemicalToChemicalAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ContributorAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ContributorAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin . + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeature ; + rdfs:subClassOf biolink:DatasetSummary ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeature . + owl:someValuesFrom biolink:DatasetSummary . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + rdfs:subClassOf biolink:IndividualOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneProductRelationship . + owl:someValuesFrom biolink:IndividualOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:RetrievalSource ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RetrievalSource . + owl:someValuesFrom biolink:GeneToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Patent ; + rdfs:subClassOf biolink:GrossAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Patent . + owl:someValuesFrom biolink:GrossAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessedMaterial ; + rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessedMaterial . + owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Treatment ; + rdfs:subClassOf biolink:GenomicSequenceLocalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Treatment . + owl:someValuesFrom biolink:GenomicSequenceLocalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:VariantToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:VariantToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:Patent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:Patent . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToDiseaseAssociation ; + rdfs:subClassOf biolink:DrugToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToDiseaseAssociation . + owl:someValuesFrom biolink:DrugToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalStructure . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathologicalEntityMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; + rdfs:subClassOf biolink:VariantToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + owl:someValuesFrom biolink:VariantToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . + owl:someValuesFrom biolink:GeneProductIsoformMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalIntervention ; + rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalIntervention . + owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . [] a owl:Restriction ; - rdfs:subClassOf biolink:Serial ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Serial . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyResult ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyResult . + owl:someValuesFrom biolink:SequenceFeatureRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:Plant ; + rdfs:subClassOf biolink:BookChapter ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Plant . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity . + owl:someValuesFrom biolink:BookChapter . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; + rdfs:subClassOf biolink:CellularOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . + owl:someValuesFrom biolink:CellularOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptToGeneRelationship ; + rdfs:subClassOf biolink:PopulationToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptToGeneRelationship . + owl:someValuesFrom biolink:PopulationToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; + rdfs:subClassOf biolink:LogOddsAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . + owl:someValuesFrom biolink:LogOddsAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; + rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalFinding ; + rdfs:subClassOf biolink:Food ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalFinding . + owl:someValuesFrom biolink:Food . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + rdfs:subClassOf biolink:Study ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + owl:someValuesFrom biolink:Study . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; + rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . + owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Human ; + rdfs:subClassOf biolink:ProteinDomain ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Human . + owl:someValuesFrom biolink:ProteinDomain . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismToOrganismAssociation ; + rdfs:subClassOf biolink:StudyResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismToOrganismAssociation . + owl:someValuesFrom biolink:StudyResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:AnatomicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:AnatomicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Fungus ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Fungus . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; + rdfs:subClassOf biolink:Drug ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + owl:someValuesFrom biolink:Drug . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularEntity ; + rdfs:subClassOf biolink:GeneFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularEntity . + owl:someValuesFrom biolink:GeneFamily . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon_label ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:in_taxon_label ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon . + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Dataset ; + rdfs:subClassOf biolink:GeographicLocationAtTime ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Dataset . + owl:someValuesFrom biolink:GeographicLocationAtTime . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugExposure ; + rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugExposure . + owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EpigenomicEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Invertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . + owl:someValuesFrom biolink:Invertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProductIsoform ; + rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProductIsoform . + owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineMixin . + rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; + rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalExposure . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:FoodAdditive ; + rdfs:subClassOf biolink:DatasetDistribution ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FoodAdditive . + owl:someValuesFrom biolink:DatasetDistribution . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalAttribute ; + rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalAttribute . + owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + rdfs:subClassOf biolink:SocioeconomicAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseAssociation . + owl:someValuesFrom biolink:SocioeconomicAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleosomeModification ; + rdfs:subClassOf biolink:Disease ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleosomeModification . + owl:someValuesFrom biolink:Disease . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToGoTermAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToGoTermAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RegulatoryRegion ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RegulatoryRegion . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicQuality ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicQuality . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence . + owl:someValuesFrom biolink:OntologyClass . [] a owl:Restriction ; - rdfs:subClassOf biolink:Haplotype ; + rdfs:subClassOf biolink:Protein ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Haplotype . + owl:someValuesFrom biolink:Protein . [] a owl:Restriction ; - rdfs:subClassOf biolink:SmallMolecule ; + rdfs:subClassOf biolink:ClinicalCourse ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SmallMolecule . + owl:someValuesFrom biolink:ClinicalCourse . [] a owl:Restriction ; - rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; + rdfs:subClassOf biolink:RNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . + owl:someValuesFrom biolink:RNAProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; + rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:RelationshipQuantifier . + rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EvidenceType ; + rdfs:subClassOf biolink:ReactionToCatalystAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EvidenceType . + owl:someValuesFrom biolink:ReactionToCatalystAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + rdfs:subClassOf biolink:ClinicalTrial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + owl:someValuesFrom biolink:ClinicalTrial . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genome ; + rdfs:subClassOf biolink:OrganismToOrganismAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genome . + owl:someValuesFrom biolink:OrganismToOrganismAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugLabel ; + rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugLabel . + owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ] ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Phenomenon ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Phenomenon . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptionFactorBindingSite . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneInteractionExposure . + owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:AccessibleDnaRegion ; + rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AccessibleDnaRegion . + owl:someValuesFrom biolink:EnvironmentalFoodContaminant . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genotype ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genotype . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToParticipantAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToParticipantAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Procedure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Procedure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularComplex ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularComplex . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CodingSequence ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CodingSequence . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ReagentTargetedGene ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReagentTargetedGene . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalMixture ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalMixture . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SensitivityQuantifier . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Polypeptide ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Polypeptide . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CellularComponent ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularComponent . + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . [] a owl:Restriction ; rdfs:subClassOf biolink:TaxonToTaxonAssociation ; @@ -13216,147 +13003,126 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:TaxonToTaxonAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismAttribute ; + rdfs:subClassOf biolink:Zygosity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismAttribute . + owl:someValuesFrom biolink:Zygosity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:PreprintPublication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:PreprintPublication . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; + rdfs:subClassOf biolink:Fungus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToPathwayAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . + owl:someValuesFrom biolink:Fungus . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity . + rdfs:subClassOf biolink:PairwiseMolecularInteraction ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PairwiseMolecularInteraction . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass . + owl:someValuesFrom biolink:PhysicalEssence . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + rdfs:subClassOf biolink:ChemicalRole ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + owl:someValuesFrom biolink:ChemicalRole . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalMeasurement ; + rdfs:subClassOf biolink:Human ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalMeasurement . + owl:someValuesFrom biolink:Human . [] a owl:Restriction ; - rdfs:subClassOf biolink:Agent ; + rdfs:subClassOf biolink:VariantToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Agent . + owl:someValuesFrom biolink:VariantToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationToPopulationAssociation ; + rdfs:subClassOf biolink:GenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationToPopulationAssociation . + owl:someValuesFrom biolink:GenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalSex ; + rdfs:subClassOf biolink:MolecularActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalSex . + owl:someValuesFrom biolink:MolecularActivity . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin . + owl:someValuesFrom biolink:ActivityAndBehavior . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPathwayAssociation ; + rdfs:subClassOf biolink:Virus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPathwayAssociation . + owl:someValuesFrom biolink:Virus . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; + rdfs:subClassOf biolink:OrganismAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . + owl:someValuesFrom biolink:OrganismAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:Transcript ; + rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Transcript . + owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Article ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Article . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetDistribution ; + rdfs:subClassOf biolink:TranscriptToGeneRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetDistribution . + owl:someValuesFrom biolink:TranscriptToGeneRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:PreprintPublication ; + rdfs:subClassOf biolink:Device ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PreprintPublication . + owl:someValuesFrom biolink:Device . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConfidenceLevel ; + rdfs:subClassOf biolink:BehavioralExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConfidenceLevel . + owl:someValuesFrom biolink:BehavioralExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSample ; + rdfs:subClassOf biolink:Book ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSample . + owl:someValuesFrom biolink:Book . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetSummary ; + rdfs:subClassOf biolink:PosttranslationalModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetSummary . + owl:someValuesFrom biolink:PosttranslationalModification . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Outcome . + rdfs:subClassOf biolink:ClinicalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Food ; + rdfs:subClassOf biolink:NucleicAcidEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Food . + owl:someValuesFrom biolink:NucleicAcidEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneticInheritance ; + rdfs:subClassOf biolink:Agent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneticInheritance . + owl:someValuesFrom biolink:Agent . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + rdfs:subClassOf biolink:AdministrativeEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + owl:someValuesFrom biolink:AdministrativeEntity . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; @@ -13364,109 +13130,95 @@ biolink:subject a owl:ObjectProperty ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathognomonicityQuantifier . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Study ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Study . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Case ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin . + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; + rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChiSquaredAnalysisResult . + owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularOrganism ; + rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularOrganism . + owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BioticExposure ; + rdfs:subClassOf biolink:MicroRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BioticExposure . + owl:someValuesFrom biolink:MicroRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; + rdfs:subClassOf biolink:NoncodingRNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . + owl:someValuesFrom biolink:NoncodingRNAProduct . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent . + rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFeature ; + rdfs:subClassOf biolink:ExonToTranscriptRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFeature . + owl:someValuesFrom biolink:ExonToTranscriptRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThing ; + rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThing . + owl:someValuesFrom biolink:ChemicalToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcess ; + rdfs:subClassOf biolink:Activity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcess . + owl:someValuesFrom biolink:Activity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Behavior ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Behavior . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:FoodAdditive ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:FoodAdditive . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicSex ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicSex . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Plant ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Plant . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:Onset ; @@ -13474,125 +13226,194 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Onset . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyVariable ; + rdfs:subClassOf biolink:CommonDataElement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyVariable . + owl:someValuesFrom biolink:CommonDataElement . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalExposure ; + rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalExposure . + owl:someValuesFrom biolink:TranscriptionFactorBindingSite . [] a owl:Restriction ; - rdfs:subClassOf biolink:AdministrativeEntity ; + rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AdministrativeEntity . + owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct . + rdfs:subClassOf biolink:ChemicalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Mammal ; + rdfs:subClassOf biolink:NamedThing ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Mammal . + owl:someValuesFrom biolink:NamedThing . [] a owl:Restriction ; - rdfs:subClassOf biolink:Gene ; + rdfs:subClassOf biolink:Polypeptide ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Gene . + owl:someValuesFrom biolink:Polypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:PlanetaryEntity ; + rdfs:subClassOf biolink:ProteinFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PlanetaryEntity . + owl:someValuesFrom biolink:ProteinFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:IndividualOrganism ; + rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:IndividualOrganism . + owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToPathwayAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToPathwayAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ProteinIsoform ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ProteinIsoform . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BehavioralFeature ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BehavioralFeature . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EvidenceType ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EvidenceType . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene_or_gene_product ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneGroupingMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ClinicalFinding ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalFinding . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . + owl:someValuesFrom biolink:PathologicalAnatomicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalEntity ; + rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalEntity . + owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalCourse ; + rdfs:subClassOf biolink:Genome ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalCourse . + owl:someValuesFrom biolink:Genome . [] a owl:Restriction ; - rdfs:subClassOf biolink:FunctionalAssociation ; + rdfs:subClassOf biolink:Hospitalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FunctionalAssociation . + owl:someValuesFrom biolink:Hospitalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPopulationAssociation ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPopulationAssociation . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexMolecularMixture ; + rdfs:subClassOf biolink:Article ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexMolecularMixture . + owl:someValuesFrom biolink:Article . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; + rdfs:subClassOf biolink:Cohort ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + owl:someValuesFrom biolink:Cohort . [] a owl:Restriction ; - rdfs:subClassOf biolink:MicroRNA ; + rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MicroRNA . + owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcessExposure ; + rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcessExposure . + owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; + rdfs:subClassOf biolink:Serial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . + owl:someValuesFrom biolink:Serial . [] a owl:Restriction ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; + rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NoncodingRNAProduct . + owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:subject ] ; + owl:allValuesFrom ; + owl:onProperty biolink:frequency_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:FrequencyQualifierMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneticInheritance ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneticInheritance . [] a owl:Restriction ; rdfs:subClassOf biolink:Event ; @@ -13600,151 +13421,135 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Event . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalModifier ; + rdfs:subClassOf biolink:ClinicalAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalModifier . + owl:someValuesFrom biolink:ClinicalAttribute . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SpecificityQuantifier . + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . + rdfs:subClassOf biolink:OrganismalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysiologicalProcess ; + rdfs:subClassOf biolink:Case ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysiologicalProcess . + owl:someValuesFrom biolink:Case . [] a owl:Restriction ; - rdfs:subClassOf biolink:Protein ; + rdfs:subClassOf biolink:TextMiningResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Protein . + owl:someValuesFrom biolink:TextMiningResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneAssociation ; + rdfs:subClassOf biolink:ChemicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneAssociation . + owl:someValuesFrom biolink:ChemicalEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeographicExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeographicExposure . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:SubjectOfInvestigation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicSex ; + rdfs:subClassOf biolink:GeneToGeneProductRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicSex . + owl:someValuesFrom biolink:GeneToGeneProductRelationship . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Snv ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Snv . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Entity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Entity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BiologicalProcessOrActivity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Attribute ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Attribute . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:has_biological_sequence ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . + owl:someValuesFrom biolink:GenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:ComplexMolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:ComplexMolecularMixture . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:AccessibleDnaRegion ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:AccessibleDnaRegion . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ReagentTargetedGene ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ReagentTargetedGene . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RNAProductIsoform ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RNAProductIsoform . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:InformationContentEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:InformationContentEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiagnosticAid ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiagnosticAid . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -13752,209 +13557,211 @@ biolink:subject a owl:ObjectProperty ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalEntity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:SiRNA ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SiRNA . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CommonDataElement ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CommonDataElement . + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PosttranslationalModification ; + rdfs:subClassOf biolink:RetrievalSource ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PosttranslationalModification . + owl:someValuesFrom biolink:RetrievalSource . [] a owl:Restriction ; - rdfs:subClassOf biolink:Exon ; + rdfs:subClassOf biolink:DrugLabel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Exon . + owl:someValuesFrom biolink:DrugLabel . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_gene_or_gene_product ], + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_total ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + owl:someValuesFrom biolink:FrequencyQuantifier . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; owl:allValuesFrom xsd:time ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:timepoint ] ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CellLine ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLine . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicExposure ; + rdfs:subClassOf biolink:WebPage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicExposure . + owl:someValuesFrom biolink:WebPage . [] a owl:Restriction ; - rdfs:subClassOf biolink:Disease ; + rdfs:subClassOf biolink:MolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Disease . + owl:someValuesFrom biolink:MolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:JournalArticle ; + rdfs:subClassOf biolink:Bacterium ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:JournalArticle . + owl:someValuesFrom biolink:Bacterium . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MaterialSample ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:synonym ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGeneAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Zygosity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Zygosity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ] ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . + owl:someValuesFrom biolink:DrugToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MacromolecularComplex ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MacromolecularComplex . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EntityToDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SmallMolecule ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SmallMolecule . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxon ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxon . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathognomonicityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntity ; + rdfs:subClassOf biolink:ProcessedMaterial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntity . + owl:someValuesFrom biolink:ProcessedMaterial . [] a owl:Restriction ; - rdfs:subClassOf biolink:LogOddsAnalysisResult ; + rdfs:subClassOf biolink:MaterialSample ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LogOddsAnalysisResult . + owl:someValuesFrom biolink:MaterialSample . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; @@ -13964,230 +13771,329 @@ biolink:subject a owl:ObjectProperty ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin . + owl:someValuesFrom biolink:GeneToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; + rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneAssociation . + owl:someValuesFrom biolink:DrugToGeneInteractionExposure . [] a owl:Restriction ; rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; owl:onProperty biolink:category ; owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin . - [] a owl:Restriction ; rdfs:subClassOf biolink:Association ; owl:onProperty biolink:category ; owl:someValuesFrom biolink:Association . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidEntity ; + rdfs:subClassOf biolink:GenotypeToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidEntity . + owl:someValuesFrom biolink:GenotypeToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalAssociation . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; + rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . + owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ContributorAssociation ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:xref ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneProductMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ContributorAssociation . + owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Vertebrate ; + rdfs:subClassOf biolink:EnvironmentalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Vertebrate . + owl:someValuesFrom biolink:EnvironmentalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalExposure ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GenotypeToVariantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalExposure . + owl:someValuesFrom biolink:GenotypeToVariantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularMixture ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularMixture . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:SiRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:SiRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ClinicalMeasurement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ClinicalMeasurement . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypicSex ; + rdfs:subClassOf biolink:ChemicalMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypicSex . + owl:someValuesFrom biolink:ChemicalMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:Pathway ; + rdfs:subClassOf biolink:Gene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Pathway . + owl:someValuesFrom biolink:Gene . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:PlanetaryEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + owl:someValuesFrom biolink:PlanetaryEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Case ; + rdfs:subClassOf biolink:FunctionalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Case . + owl:someValuesFrom biolink:FunctionalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneExpressionMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Outcome ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SequenceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + owl:someValuesFrom biolink:SequenceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyPopulation ; + rdfs:subClassOf biolink:SeverityValue ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyPopulation . + owl:someValuesFrom biolink:SeverityValue . [] a owl:Restriction ; - rdfs:subClassOf biolink:Bacterium ; + rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Bacterium . + owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Dataset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Dataset . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToVariantAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToVariantAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:GrossAnatomicalStructure ; + rdfs:subClassOf biolink:PathologicalProcessExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GrossAnatomicalStructure . + owl:someValuesFrom biolink:PathologicalProcessExposure . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseMolecularInteraction ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseMolecularInteraction . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinDomain ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinDomain . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; + rdfs:subClassOf biolink:SocioeconomicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . + owl:someValuesFrom biolink:SocioeconomicExposure . [] a owl:Restriction ; rdfs:subClassOf biolink:Cell ; @@ -14195,24 +14101,27 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Cell . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ExonToTranscriptRelationship ; + rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExonToTranscriptRelationship . + owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:BiologicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:BiologicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Snv ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Snv . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineMixin . [] a owl:Restriction ; rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; @@ -14220,29 +14129,9 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Invertebrate ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Invertebrate . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalRole ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalRole . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Cohort ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cohort . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProduct ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProduct . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneFamily ; + rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneFamily . + owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:Publication ; @@ -14250,58 +14139,86 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Publication . [] a owl:Restriction ; - rdfs:subClassOf biolink:SeverityValue ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SeverityValue . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinIsoform ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinIsoform . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + rdfs:subClassOf biolink:PhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + owl:someValuesFrom biolink:PhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGoTermAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGoTermAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Outcome . [] a owl:Restriction ; - rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:DrugExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . + owl:someValuesFrom biolink:DrugExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon_label ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ThingWithTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:RegulatoryRegion ; + rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RegulatoryRegion . + owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + rdfs:subClassOf biolink:ClinicalModifier ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior . + owl:someValuesFrom biolink:ClinicalModifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralExposure ; + rdfs:subClassOf biolink:Genotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralExposure . + owl:someValuesFrom biolink:Genotype . [] a owl:Restriction ; rdfs:subClassOf biolink:ConceptCountAnalysisResult ; @@ -14309,14 +14226,9 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:ConceptCountAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + rdfs:subClassOf biolink:ClinicalIntervention ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . + owl:someValuesFrom biolink:ClinicalIntervention . [] a owl:Restriction ; rdfs:subClassOf biolink:PhysicalEntity ; @@ -14324,225 +14236,313 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:PhysicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Activity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Activity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Attribute ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Attribute . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetVersion ; + rdfs:subClassOf biolink:PhysiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetVersion . + owl:someValuesFrom biolink:PhysiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:BioticExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:BioticExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; + rdfs:subClassOf biolink:MolecularEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . + owl:someValuesFrom biolink:MolecularEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; + rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Device ; + rdfs:subClassOf biolink:ReactionToParticipantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Device . + owl:someValuesFrom biolink:ReactionToParticipantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralFeature ; + rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralFeature . + owl:someValuesFrom biolink:NucleicAcidSequenceMotif . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicAttribute ; + rdfs:subClassOf biolink:Exon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicAttribute . + owl:someValuesFrom biolink:Exon . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcess ; + rdfs:subClassOf biolink:CellLine ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcess . + owl:someValuesFrom biolink:CellLine . [] a owl:Restriction ; - rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; + rdfs:subClassOf biolink:CellularComponent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . + owl:someValuesFrom biolink:CellularComponent . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Outcome ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicBackgroundExposure ; + rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicBackgroundExposure . + owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiagnosticAid ; + rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiagnosticAid . + owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidSequenceMotif . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Virus ; + rdfs:subClassOf biolink:Mammal ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Virus . + owl:someValuesFrom biolink:Mammal . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; + rdfs:subClassOf biolink:CodingSequence ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . + owl:someValuesFrom biolink:CodingSequence . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CellLine ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:LifeStage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . + owl:someValuesFrom biolink:LifeStage . [] a owl:Restriction ; - rdfs:subClassOf biolink:BookChapter ; + rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BookChapter . + owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Case ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . + owl:someValuesFrom biolink:CaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:BiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . + owl:someValuesFrom biolink:BiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexChemicalExposure ; + rdfs:subClassOf biolink:PathologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexChemicalExposure . + owl:someValuesFrom biolink:PathologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntity ; + rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntity . + owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:StudyVariable ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:StudyVariable . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EnvironmentalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EnvironmentalExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BiologicalSex ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BiologicalSex . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChiSquaredAnalysisResult . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:RelationshipQuantifier . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ] ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . + owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . + owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ConfidenceLevel ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ConfidenceLevel . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Treatment ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Treatment . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . diff --git a/project/prefixmap/biolink-model-prefix-map.json b/project/prefixmap/biolink-model-prefix-map.json index ffc9dfb5e..5319bdeff 100644 --- a/project/prefixmap/biolink-model-prefix-map.json +++ b/project/prefixmap/biolink-model-prefix-map.json @@ -259,4 +259,4 @@ "skos": "http://www.w3.org/2004/02/skos/core#", "wgs": "http://www.w3.org/2003/01/geo/wgs84_pos", "xsd": "http://www.w3.org/2001/XMLSchema#" -} +} \ No newline at end of file diff --git a/project/protobuf/biolink_model.proto b/project/protobuf/biolink_model.proto index e8052a941..8dd5b8b2d 100644 --- a/project/protobuf/biolink_model.proto +++ b/project/protobuf/biolink_model.proto @@ -1,3 +1,7 @@ + syntax="proto3"; + package +// metamodel_version: 1.7.0 +// version: 4.2.4 // A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose message AccessibleDnaRegion { diff --git a/project/shacl/biolink_model.shacl.ttl b/project/shacl/biolink_model.shacl.ttl index 8a16f0947..baf90d365 100644 --- a/project/shacl/biolink_model.shacl.ttl +++ b/project/shacl/biolink_model.shacl.ttl @@ -10,66 +10,88 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ] ; sh:targetClass biolink:AccessibleDnaRegion . @@ -79,54 +101,72 @@ biolink:Activity a sh:NodeShape ; sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; @@ -137,165 +177,220 @@ biolink:ActivityAndBehavior a sh:NodeShape ; biolink:AdministrativeEntity a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; + sh:ignoredProperties ( biolink:address biolink:affiliation rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:AdministrativeEntity . biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:AnatomicalEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -303,29 +398,17 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:AnatomicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -333,84 +416,74 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ] ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:AnatomicalEntity ; sh:description "the structure at an earlier time" ; sh:maxCount 1 ; @@ -418,44 +491,45 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -465,294 +539,214 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the part" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at a later time" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:AnatomicalEntity ; sh:description "the whole" ; sh:maxCount 1 ; @@ -760,35 +754,189 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the part" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . biolink:Annotation a sh:NodeShape ; sh:closed false ; sh:description "Biolink Model root class for entity annotations." ; - sh:ignoredProperties ( rdf:type ) ; + sh:ignoredProperties ( biolink:has_unit rdf:type biolink:has_numeric_value ) ; sh:targetClass biolink:Annotation . biolink:Article a sh:NodeShape ; @@ -796,252 +944,303 @@ biolink:Article a sh:NodeShape ; sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 7 ; - sh:path biolink:keywords ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:issue ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:category ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:volume ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:order 21 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 15 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:creation_date ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:license ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 17 ; - sh:path biolink:synonym ], + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:deprecated ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:summary ], + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:published_in ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:iri ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 10 ; - sh:path dct:type ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:rights ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:issue ] ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path dct:type ] ; sh:targetClass biolink:Article . biolink:Association a sh:NodeShape ; sh:closed true ; sh:description "A typed association between two entities, supported by evidence" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:ignoredProperties ( biolink:phase biolink:associated_environmental_context biolink:population_context_qualifier biolink:clinical_approval_status biolink:has_quotient biolink:start_interbase_coordinate rdf:type biolink:reaction_side biolink:interacting_molecules_category biolink:object_form_or_variant_qualifier biolink:stoichiometry biolink:FDA_adverse_event_level biolink:object_context_qualifier biolink:onset_qualifier biolink:subject_derivative_qualifier biolink:subject_direction_qualifier biolink:quantifier_qualifier biolink:expression_site biolink:max_research_phase biolink:reaction_direction biolink:frequency_qualifier biolink:phenotypic_state biolink:object_aspect_qualifier biolink:anatomical_context_qualifier biolink:object_derivative_qualifier biolink:subject_form_or_variant_qualifier biolink:stage_qualifier biolink:strand biolink:causal_mechanism_qualifier biolink:subject_part_qualifier biolink:has_count biolink:species_context_qualifier biolink:catalyst_qualifier biolink:object_part_qualifier biolink:has_percentage biolink:genome_build biolink:has_total biolink:subject_context_qualifier biolink:temporal_context_qualifier biolink:qualified_predicate biolink:end_interbase_coordinate biolink:sex_qualifier biolink:object_direction_qualifier biolink:subject_aspect_qualifier ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -1050,379 +1249,450 @@ biolink:Association a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ] ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:Association . biolink:Bacterium a sh:NodeShape ; sh:closed true ; sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Bacterium . biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 46 ; sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:BehavioralFeature ; + sh:description "behavioral feature that is the object of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:BehavioralFeature ; - sh:description "behavioral feature that is the object of the association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Behavior ; + sh:description "behavior that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ] ; + sh:path biolink:p_value ] ; sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . biolink:BehavioralExposure a sh:NodeShape ; @@ -1430,37 +1700,29 @@ biolink:BehavioralExposure a sh:NodeShape ; sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -1475,29 +1737,57 @@ biolink:BehavioralExposure a sh:NodeShape ; sh:order 2 ; sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ] ; sh:targetClass biolink:BehavioralExposure . @@ -1510,274 +1800,338 @@ biolink:BehavioralOutcome a sh:NodeShape ; biolink:BiologicalEntity a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; + sh:ignoredProperties ( biolink:has_zygosity biolink:enabled_by biolink:has_input biolink:symbol biolink:has_biological_sequence rdf:type biolink:has_output biolink:has_gene biolink:has_gene_or_gene_product ) ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:BiologicalEntity . biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:closed true ; sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_input ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:enabled_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:has_output ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:has_output ] ; + sh:targetClass biolink:BiologicalProcessOrActivity . + +biolink:BioticExposure a sh:NodeShape ; + sh:closed true ; + sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:BiologicalProcessOrActivity . - -biolink:BioticExposure a sh:NodeShape ; - sh:closed true ; - sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "a point in time" ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:BioticExposure . biolink:Book a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Books should have industry-standard identifier such as from ISBN." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:creation_date ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:keywords ], [ sh:class biolink:Attribute ; @@ -1785,113 +2139,155 @@ biolink:Book a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:rights ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:format ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Books should have industry-standard identifier such as from ISBN." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Book . biolink:BookChapter a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "chapter of a book" ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:chapter ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:rights ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:description "mesh terms tagging a publication" ; + sh:description "chapter of a book" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:chapter ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:mesh_terms ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:volume ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:summary ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 16 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:published_in ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; @@ -1899,120 +2295,136 @@ biolink:BookChapter a sh:NodeShape ; sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:volume ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 20 ; - sh:path rdf:type ], + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 9 ; - sh:path dct:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path dct:description ] ; sh:targetClass biolink:BookChapter . biolink:CaseToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An abstract association for use where the case is the subject" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:class biolink:Case ; sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:CaseToEntityAssociationMixin . biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -2020,737 +2432,869 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:object_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ] ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to cause the disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_count ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to cause the disease." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:has_total ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ] ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ] ; sh:targetClass biolink:CausalGeneToDiseaseAssociation . biolink:Cell a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Cell . biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "The relationship to the disease" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -2761,216 +3305,241 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; - sh:ignoredProperties ( rdf:type ) ; + sh:ignoredProperties ( biolink:subject_direction_qualifier biolink:object_aspect_qualifier biolink:qualified_predicate rdf:type biolink:frequency_qualifier biolink:object_direction_qualifier biolink:subject_aspect_qualifier ) ; sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ] ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ] ; sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An relationship between a cell line and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:CellLine ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; @@ -2979,150 +3548,146 @@ biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:object ], + [ sh:class biolink:CellLine ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:CellLineToEntityAssociationMixin . biolink:CellularOrganism a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; + sh:path rdf:type ] ; sh:targetClass biolink:CellularOrganism . biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 52 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 36 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 17 ; - sh:path rdf:object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 48 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_evidence ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:object_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 50 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 49 ; - sh:path rdf:type ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; @@ -3130,325 +3695,334 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 51 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:knowledge_level ], + sh:order 52 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 53 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:original_object ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:negated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 17 ; + sh:path rdf:object ], [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:in ( "metabolite" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:subject_derivative_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:negated ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:AnatomicalEntity ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:p_value ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], + sh:order 14 ; + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 25 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:object_context_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 45 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 11 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 46 ; - sh:path biolink:id ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:original_object ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 34 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 41 ; - sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:species_context_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 12 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:ChemicalAffectsGeneAssociation . - -biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:timepoint ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 37 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:has_evidence ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:subject_context_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:object_part_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:qualifiers ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 32 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 45 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:ChemicalAffectsGeneAssociation . + +biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -3456,148 +4030,208 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . - -biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A regulatory relationship between two genes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:order 37 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:original_predicate ], + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; - sh:path biolink:id ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . + +biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A regulatory relationship between two genes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -3605,123 +4239,176 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:nodeKind sh:BlankNodeOrIRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:description "the direction is always from regulator to regulated" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "the direction is always from regulator to regulated" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdf:predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; @@ -3741,9 +4428,11 @@ biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; @@ -3758,318 +4447,368 @@ biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; biolink:ChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A chemical exposure is an intake of a particular chemical entity." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:ignoredProperties ( rdf:type biolink:has_gene_or_gene_product ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 3 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:full_name ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ] ; + sh:path rdf:type ] ; sh:targetClass biolink:ChemicalExposure . biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:closed true ; sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 34 ; - sh:path biolink:object_label_closure ], + sh:order 13 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_closure ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:category ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 42 ; - sh:path rdf:type ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:knowledge_level ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 20 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path rdfs:label ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:subject_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:object_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path rdf:type ], [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:object_part_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:deprecated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 10 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:subject ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 41 ; - sh:path biolink:category ], + sh:order 45 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 18 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:negated ], [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], + sh:order 8 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 10 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 45 ; - sh:path biolink:has_attribute ] ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:ChemicalGeneInteractionAssociation . biolink:ChemicalMixture a sh:NodeShape ; @@ -4077,51 +4816,9 @@ biolink:ChemicalMixture a sh:NodeShape ; sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], [ sh:class biolink:Attribute ; @@ -4129,45 +4826,109 @@ biolink:ChemicalMixture a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:id ] ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ] ; sh:targetClass biolink:ChemicalMixture . biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; @@ -4179,93 +4940,98 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:closed true ; sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -4273,46 +5039,57 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -4320,151 +5097,276 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "a point in time" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 3 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ] ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:description "" ; sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:FDA_adverse_event_level ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; @@ -4473,313 +5375,262 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:path dct:description ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:ignoredProperties ( biolink:stoichiometry biolink:catalyst_qualifier rdf:type biolink:reaction_side biolink:reaction_direction ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:ChemicalToChemicalAssociation . biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; @@ -4787,203 +5638,233 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the upstream chemical entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the downstream chemical entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path biolink:catalyst_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the downstream chemical entity" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the upstream chemical entity" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ] ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ] ; sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; @@ -4991,99 +5872,126 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; @@ -5091,116 +5999,121 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An interaction between a chemical entity and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -5214,58 +6127,136 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a chemical entity and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that is affected by the chemical" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical entity that is affecting the pathway" ; sh:maxCount 1 ; @@ -5273,212 +6264,186 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that is affected by the chemical" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ] ; + sh:order 6 ; + sh:path biolink:publications ] ; sh:targetClass biolink:ChemicalToPathwayAssociation . biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a chi squared analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ChiSquaredAnalysisResult . biolink:ClinicalCourse a sh:NodeShape ; @@ -5486,39 +6451,31 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -5527,31 +6484,57 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:order 1 ; sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ClinicalCourse . biolink:ClinicalEntity a sh:NodeShape ; @@ -5561,180 +6544,248 @@ biolink:ClinicalEntity a sh:NodeShape ; sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ] ; + sh:path biolink:id ] ; sh:targetClass biolink:ClinicalEntity . biolink:ClinicalFinding a sh:NodeShape ; sh:closed true ; sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:ClinicalAttribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:ClinicalFinding . - -biolink:ClinicalIntervention a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; + [ sh:class biolink:ClinicalAttribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:ClinicalFinding . + +biolink:ClinicalIntervention a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ClinicalIntervention . biolink:ClinicalMeasurement a sh:NodeShape ; sh:closed true ; sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -5742,89 +6793,91 @@ biolink:ClinicalMeasurement a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ] ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ] ; sh:targetClass biolink:ClinicalMeasurement . biolink:ClinicalModifier a sh:NodeShape ; sh:closed true ; sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -5837,16 +6890,27 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:order 3 ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -5854,142 +6918,193 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ] ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ] ; sh:targetClass biolink:ClinicalModifier . biolink:ClinicalTrial a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path rdf:type ] ; - sh:targetClass biolink:ClinicalTrial . - -biolink:CodingSequence a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:ClinicalTrial . + +biolink:CodingSequence a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ] ; sh:targetClass biolink:CodingSequence . @@ -5998,307 +7113,389 @@ biolink:Cohort a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Cohort . biolink:CommonDataElement a sh:NodeShape ; sh:closed true ; sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:deprecated ] ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:CommonDataElement . biolink:ComplexChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ] ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ] ; sh:targetClass biolink:ComplexChemicalExposure . biolink:ComplexMolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:id ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:xref ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ] ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ] ; sh:targetClass biolink:ComplexMolecularMixture . biolink:ConceptCountAnalysisResult a sh:NodeShape ; @@ -6306,259 +7503,302 @@ biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ConceptCountAnalysisResult . biolink:ConfidenceLevel a sh:NodeShape ; sh:closed true ; sh:description "Level of confidence in a statement" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ] ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ConfidenceLevel . biolink:ContributorAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Agent ; - sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; @@ -6569,68 +7809,80 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Agent ; + sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:InformationContentEntity ; sh:description "information content entity which an agent has helped realise" ; sh:maxCount 1 ; @@ -6639,130 +7891,115 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ] ; + sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ] ; sh:targetClass biolink:ContributorAssociation . biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:float ; + sh:property [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -6770,349 +8007,486 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to correlate with the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to correlate with the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 45 ; - sh:path biolink:has_percentage ] ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ] ; sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . biolink:DatasetSummary a sh:NodeShape ; sh:closed true ; sh:description "an item that holds summary level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:source_web_page ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:source_web_page ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path schema1:logo ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:format ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:logo ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:rights ] ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:license ] ; sh:targetClass biolink:DatasetSummary . biolink:DatasetVersion a sh:NodeShape ; sh:closed true ; sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:DatasetDistribution ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path dct:distribution ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:ingest_date ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:format ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:rights ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:deprecated ], [ sh:class biolink:Dataset ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_dataset ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:DatasetDistribution ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path dct:distribution ] ; + sh:path biolink:has_dataset ] ; sh:targetClass biolink:DatasetVersion . biolink:DiagnosticAid a sh:NodeShape ; sh:closed true ; sh:description "A device or substance used to help diagnose disease or injury" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ] ; sh:targetClass biolink:DiagnosticAid . @@ -7121,77 +8495,97 @@ biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:closed true ; sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; @@ -7203,9 +8597,11 @@ biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; @@ -7228,590 +8624,579 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:closed true ; sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:GeneticInheritance ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:GeneticInheritance ; sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 6 ; + sh:path biolink:publications ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . - -biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:DiseaseToEntityAssociationMixin . - -biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between an exposure event and a disease." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + +biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:ExposureEvent ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:DiseaseToEntityAssociationMixin . + +biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between an exposure event and a disease." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -7819,306 +9204,491 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:DiseaseToExposureEventAssociation . - -biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:double ; + sh:path rdf:predicate ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_quotient ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:adjusted_p_value ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 19 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ] ; + sh:targetClass biolink:DiseaseToExposureEventAssociation . + +biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 48 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 43 ; + sh:path biolink:has_attribute ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category ], + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 47 ; sh:path biolink:object_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:negated ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 40 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 32 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:publications ], + sh:order 23 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:category ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_total ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 43 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], + sh:order 24 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:sex_qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 37 ; - sh:path biolink:id ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], + sh:order 7 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path rdf:type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:publications ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_count ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:has_percentage ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 39 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path rdf:predicate ] ; + sh:order 17 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:iri ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:onset_qualifier ] ; sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . biolink:DrugExposure a sh:NodeShape ; sh:closed true ; sh:description "A drug exposure is an intake of a particular drug." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:ignoredProperties ( rdf:type biolink:has_gene_or_gene_product ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -8126,157 +9696,162 @@ biolink:DrugExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ] ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:DrugExposure . biolink:DrugLabel a sh:NodeShape ; sh:closed true ; sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:keywords ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path dct:type ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:format ] ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ] ; sh:targetClass biolink:DrugLabel . biolink:DrugToEntityAssociationMixin a sh:NodeShape ; @@ -8290,9 +9865,11 @@ biolink:DrugToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; @@ -8309,614 +9886,695 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Drug ; + sh:description "the drug that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product that is affected by the drug" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product that is affected by the drug" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:order 21 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:DrugToGeneAssociation . biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:closed true ; sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:class biolink:Gene ; + sh:property [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene_or_gene_product ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 4 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:provided_by ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:full_name ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 11 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ] ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ] ; sh:targetClass biolink:DrugToGeneInteractionExposure . biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "connects an association to an instance of supporting evidence" ; + sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 40 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 45 ; sh:path biolink:has_percentage ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:description "connects an association to an instance of supporting evidence" ; - sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 46 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ] ; + sh:order 9 ; + sh:path biolink:publications ] ; sh:targetClass biolink:DruggableGeneToDiseaseAssociation . biolink:Entity a sh:NodeShape ; sh:closed false ; sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; + sh:ignoredProperties ( biolink:negated biolink:highest_FDA_approval_status biolink:has_evidence biolink:has_supporting_studies biolink:resource_id rdf:type biolink:object_form_or_variant_qualifier biolink:authors biolink:has_gene biolink:upstream_resource_ids biolink:has_procedure biolink:available_from biolink:has_zygosity biolink:has_drug biolink:FDA_adverse_event_level biolink:has_qualitative_value biolink:has_input biolink:expression_site biolink:routes_of_delivery biolink:in_taxon biolink:has_taxonomic_rank biolink:subject_part_qualifier biolink:causal_mechanism_qualifier biolink:strand biolink:species_context_qualifier biolink:has_output biolink:ingest_date biolink:subject_closure biolink:has_dataset biolink:published_in biolink:latitude biolink:trade_name biolink:associated_environmental_context biolink:population_context_qualifier rdf:object biolink:original_subject biolink:has_attribute_type biolink:license biolink:agent_type biolink:start_interbase_coordinate biolink:rights biolink:original_object biolink:retrieval_source_ids biolink:xref biolink:onset_qualifier biolink:subject_direction_qualifier biolink:quantifier_qualifier biolink:subject_category_closure biolink:phenotypic_state biolink:subject_category rdf:subject biolink:aggregator_knowledge_source biolink:object_aspect_qualifier biolink:anatomical_context_qualifier biolink:p_value biolink:subject_form_or_variant_qualifier biolink:publications biolink:chapter biolink:symbol biolink:has_biological_sequence biolink:object_category biolink:issue dct:distribution biolink:genome_build biolink:in_taxon_label biolink:has_total biolink:volume biolink:temporal_context_qualifier biolink:object_namespace biolink:source_web_page biolink:affiliation biolink:object_direction_qualifier biolink:subject_aspect_qualifier biolink:has_gene_or_gene_product biolink:longitude biolink:object_label_closure biolink:phase biolink:original_predicate dct:type biolink:full_name biolink:clinical_approval_status biolink:timepoint biolink:summary biolink:interacting_molecules_category biolink:stoichiometry biolink:reaction_direction biolink:keywords biolink:object_derivative_qualifier biolink:stage_qualifier biolink:is_metabolite biolink:subject_namespace biolink:drug_regulatory_status_world_wide biolink:creation_date biolink:object_closure biolink:address biolink:object_category_closure biolink:iso_abbreviation biolink:primary_knowledge_source biolink:end_interbase_coordinate biolink:sex_qualifier schema1:logo biolink:synonym biolink:is_toxic biolink:has_quotient biolink:reaction_side biolink:max_tolerated_dose biolink:has_chemical_role biolink:is_supplement biolink:has_device biolink:has_quantitative_value biolink:object_context_qualifier biolink:adjusted_p_value biolink:subject_derivative_qualifier biolink:format biolink:mesh_terms biolink:pages biolink:qualifiers biolink:max_research_phase biolink:qualifier biolink:frequency_qualifier biolink:provided_by biolink:distribution_download_url biolink:enabled_by biolink:has_count biolink:catalyst_qualifier biolink:resource_role biolink:object_part_qualifier biolink:knowledge_level biolink:has_percentage biolink:knowledge_source biolink:subject_label_closure biolink:subject_context_qualifier rdf:predicate biolink:qualified_predicate ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 2 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Entity . - -biolink:EntityToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:qualifiers ], + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:Entity . + +biolink:EntityToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path dct:description ], [ sh:class biolink:RetrievalSource ; @@ -8924,25 +10582,65 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:max_research_phase ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -8950,80 +10648,122 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -9031,79 +10771,33 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:order 20 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ] ; + sh:path biolink:subject_label_closure ] ; sh:targetClass biolink:EntityToDiseaseAssociation . biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "mixin class for any association whose object (target node) is a disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -9114,25 +10808,44 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:object_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:predicate ] ; sh:targetClass biolink:EntityToDiseaseAssociationMixin . @@ -9140,23 +10853,25 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ] ; sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . @@ -9165,23 +10880,25 @@ biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An association between some entity and an exposure event." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ] ; sh:targetClass biolink:EntityToExposureEventAssociationMixin . @@ -9189,66 +10906,75 @@ biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for entity to disease or phenotype associations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; + sh:ignoredProperties ( biolink:has_total biolink:has_count biolink:has_quotient rdf:type biolink:has_percentage biolink:sex_qualifier ) ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:frequency_qualifier ] ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ] ; sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An association between some entity and an outcome" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Outcome ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9256,266 +10982,289 @@ biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:EntityToOutcomeAssociationMixin . biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 32 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:max_research_phase ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ] ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualified_predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:has_total ], [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], [ sh:class biolink:PhenotypicFeature ; @@ -9525,6 +11274,24 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_count ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9532,22 +11299,22 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:has_total ], + sh:order 11 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:sex_qualifier ] ; + sh:path biolink:sex_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:subject_direction_qualifier ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . biolink:EnvironmentalExposure a sh:NodeShape ; @@ -9555,33 +11322,77 @@ biolink:EnvironmentalExposure a sh:NodeShape ; sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; @@ -9591,203 +11402,207 @@ biolink:EnvironmentalExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ] ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:EnvironmentalExposure . biolink:EnvironmentalFeature a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ] ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:EnvironmentalFeature . biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:trade_name ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ] ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:trade_name ] ; sh:targetClass biolink:EnvironmentalFoodContaminant . biolink:EnvironmentalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], [ sh:class biolink:Attribute ; @@ -9796,21 +11611,50 @@ biolink:EnvironmentalProcess a sh:NodeShape ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ] ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:EnvironmentalProcess . biolink:EpidemiologicalOutcome a sh:NodeShape ; @@ -9822,8 +11666,10 @@ biolink:EpidemiologicalOutcome a sh:NodeShape ; biolink:EpigenomicEntity a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; + sh:property [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ] ; sh:targetClass biolink:EpigenomicEntity . @@ -9832,105 +11678,106 @@ biolink:Event a sh:NodeShape ; sh:closed true ; sh:description "Something that happens at a given place and time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ] ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:Event . biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:closed true ; sh:description "A transcript is formed from multiple exons" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:Exon ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -9939,72 +11786,97 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Transcript ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], [ sh:class biolink:OntologyClass ; @@ -10012,267 +11884,314 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "a point in time" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:ExonToTranscriptRelationship . biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an exposure event and an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:population_context_qualifier ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:population_context_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:id ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:adjusted_p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10281,14 +12200,21 @@ biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ] ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ExposureEventToOutcomeAssociation . biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; @@ -10296,250 +12222,289 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:has_percentage ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . @@ -10547,41 +12512,31 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for disease or phenotype to entity associations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:ignoredProperties ( biolink:has_total biolink:has_count biolink:has_quotient rdf:type biolink:has_percentage biolink:sex_qualifier ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -10595,147 +12550,204 @@ biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . biolink:Food a sh:NodeShape ; sh:closed true ; sh:description "A substance consumed by a living organism as a source of nutrition" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:deprecated ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:provided_by ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:boolean ; + [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ] ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ] ; sh:targetClass biolink:Food . biolink:FoodAdditive a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], [ sh:class biolink:ChemicalRole ; @@ -10744,85 +12756,96 @@ biolink:FoodAdditive a sh:NodeShape ; sh:order 4 ; sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ] ; sh:targetClass biolink:FoodAdditive . biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifier for frequency type associations" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:ignoredProperties ( biolink:has_total biolink:has_count biolink:subject_direction_qualifier biolink:object_aspect_qualifier biolink:has_quotient biolink:qualified_predicate rdf:type biolink:has_percentage biolink:sex_qualifier biolink:object_direction_qualifier biolink:subject_aspect_qualifier ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:frequency_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:FrequencyQualifierMixin . biolink:FrequencyQuantifier a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:integer ; + sh:property [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_count ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:has_total ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:double ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:has_quotient ] ; sh:targetClass biolink:FrequencyQuantifier . @@ -10831,216 +12854,239 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "a point in time" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:publications ] ; sh:targetClass biolink:FunctionalAssociation . biolink:Fungus a sh:NodeShape ; sh:closed true ; sh:description "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], [ sh:class biolink:Attribute ; @@ -11049,43 +13095,70 @@ biolink:Fungus a sh:NodeShape ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ] ; sh:targetClass biolink:Fungus . @@ -11094,342 +13167,426 @@ biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:negated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 16 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:subject_label_closure ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 8 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 51 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path rdf:object ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 49 ; - sh:path biolink:category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 36 ; - sh:path biolink:object_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:object_category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:order 33 ; + sh:path biolink:subject_category ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:subject_closure ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:species_context_qualifier ], + sh:order 13 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 47 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:qualifier ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 54 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:adjusted_p_value ], [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:in ( "metabolite" ) ; sh:maxCount 1 ; sh:order 11 ; sh:path biolink:object_derivative_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 46 ; - sh:path biolink:has_supporting_studies ], + sh:order 22 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:knowledge_source ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 27 ; sh:path biolink:knowledge_level ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 54 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:subject_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:timepoint ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 34 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 41 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:AnatomicalEntity ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:species_context_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 43 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 42 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_namespace ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 52 ; - sh:path dct:description ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:qualifier ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path rdf:object ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:order 21 ; + sh:path biolink:qualifiers ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:order 7 ; + sh:path biolink:object_part_qualifier ], [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; sh:order 0 ; sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 35 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 53 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 28 ; sh:path biolink:agent_type ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 50 ; - sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:original_object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path dct:description ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 46 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 16 ; - sh:path rdf:subject ] ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 53 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GeneAffectsChemicalAssociation . biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:double ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:has_quotient ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 37 ; sh:path rdf:type ], [ sh:class biolink:BiologicalSex ; @@ -11438,219 +13595,205 @@ biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:sex_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:publications ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:has_supporting_studies ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_count ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ] ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ] ; sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . biolink:GeneExpressionMixin a sh:NodeShape ; sh:closed false ; sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:property [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:stage_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:phenotypic_state ] ; + sh:path biolink:phenotypic_state ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ] ; sh:targetClass biolink:GeneExpressionMixin . biolink:GeneGroupingMixin a sh:NodeShape ; @@ -11667,65 +13810,39 @@ biolink:GeneGroupingMixin a sh:NodeShape ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_total ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -11733,206 +13850,277 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 6 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:double ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_quotient ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], + sh:order 5 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 49 ; sh:path biolink:qualified_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_count ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 40 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:deprecated ], + sh:order 47 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ] ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . biolink:GeneProductIsoformMixin a sh:NodeShape ; sh:closed false ; sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:synonym ] ; sh:targetClass biolink:GeneProductIsoformMixin . @@ -11941,739 +14129,846 @@ biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 41 ; sh:path biolink:has_attribute ], + [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:species_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path dct:description ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:object_direction_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; sh:path rdfs:label ], - [ sh:description "a point in time" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:negated ] ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:GeneRegulatesGeneAssociation . biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:ignoredProperties ( rdf:type biolink:subject_form_or_variant_qualifier ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:qualified_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:publications ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 33 ; + sh:path biolink:has_supporting_studies ] ; + sh:targetClass biolink:GeneToDiseaseAssociation . + +biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type biolink:subject_form_or_variant_qualifier ) ; + sh:property [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ] ; - sh:targetClass biolink:GeneToDiseaseAssociation . - -biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 46 ; sh:path biolink:subject_direction_qualifier ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 45 ; sh:path biolink:has_percentage ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; sh:path dct:description ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 27 ; - sh:path biolink:object_namespace ] ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . biolink:GeneToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene that is the subject of the association" ; sh:maxCount 1 ; @@ -12681,95 +14976,131 @@ biolink:GeneToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:GeneToEntityAssociationMixin . biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:LifeStage ; - sh:description "stage at which the gene is expressed in the site" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:description "a point in time" ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:AnatomicalEntity ; sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; @@ -12777,195 +15108,226 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "expression relationship" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:LifeStage ; + sh:description "stage at which the gene is expressed in the site" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:stage_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:description "can be used to indicate magnitude, or also ranking" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:order 1 ; + sh:path biolink:quantifier_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "expression relationship" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeneToExpressionSiteAssociation . biolink:GeneToGeneAssociation a sh:NodeShape ; sh:closed false ; sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; - sh:ignoredProperties ( rdf:type ) ; + sh:ignoredProperties ( biolink:stage_qualifier biolink:quantifier_qualifier biolink:expression_site rdf:type biolink:interacting_molecules_category biolink:phenotypic_state ) ; sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -12973,312 +15335,295 @@ biolink:GeneToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a human-readable description of an entity" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:GeneToGeneAssociation . biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:closed true ; sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], + sh:order 41 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], [ sh:class biolink:AnatomicalEntity ; sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:expression_site ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:stage_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:phenotypic_state ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -13286,39 +15631,81 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 4 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 34 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 6 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ] ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_object ] ; sh:targetClass biolink:GeneToGeneCoexpressionAssociation . biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; @@ -13326,580 +15713,547 @@ biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "membership of the gene in the given gene family." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "membership of the gene in the given gene family." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:GeneToGeneFamilyAssociation . - -biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:description "homology relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:GeneFamily ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:GeneToGeneFamilyAssociation . + +biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:id ] ; - sh:targetClass biolink:GeneToGeneHomologyAssociation . - -biolink:GeneToGeneProductRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A gene is transcribed and potentially translated to a gene product" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "homology relationship type" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:GeneProductMixin ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:publications ], + sh:path biolink:publications ] ; + sh:targetClass biolink:GeneToGeneHomologyAssociation . + +biolink:GeneToGeneProductRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "A gene is transcribed and potentially translated to a gene product" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:Gene ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -13908,212 +16262,365 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ] ; - sh:targetClass biolink:GeneToGeneProductRelationship . - -biolink:GeneToGoTermAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:GeneProductMixin ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ] ; + sh:targetClass biolink:GeneToGeneProductRelationship . + +biolink:GeneToGoTermAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Gene ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ] ; sh:targetClass biolink:GeneToGoTermAssociation . biolink:GeneToPathwayAssociation a sh:NodeShape ; @@ -14123,136 +16630,192 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:property [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Pathway ; + sh:description "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the gene or gene product entity that participates or influences the pathway" ; sh:maxCount 1 ; @@ -14262,55 +16825,29 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that includes or is affected by the gene or gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ] ; sh:targetClass biolink:GeneToPathwayAssociation . @@ -14318,423 +16855,509 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:qualifier ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:deprecated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:has_total ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:publications ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path rdfs:label ], - [ sh:datatype xsd:double ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_count ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 37 ; sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ] ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ] ; sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . biolink:Genome a sh:NodeShape ; sh:closed true ; sh:description "A genome is the sum of genetic material within a cell or virion." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Genome . biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:closed true ; sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:xref ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_gene_or_gene_product ], + sh:order 7 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:deprecated ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 8 ; sh:path biolink:has_quantitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 14 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 12 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ] ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ] ; sh:targetClass biolink:GenomicBackgroundExposure . biolink:GenomicEntity a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; + sh:property [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ] ; sh:targetClass biolink:GenomicEntity . @@ -14744,683 +17367,792 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 38 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 39 ; - sh:path rdf:type ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:start_interbase_coordinate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; - sh:in ( "+" "-" "." "?" ) ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:strand ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:object_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path rdf:predicate ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:end_interbase_coordinate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 36 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 17 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:deprecated ], - [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; - sh:in ( "+" "-" "." "?" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:genome_build ] ; - sh:targetClass biolink:GenomicSequenceLocalization . - -biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 22 ; sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:end_interbase_coordinate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + sh:in ( "0" "1" "2" ) ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], + sh:order 4 ; + sh:path biolink:phase ], + [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; + sh:in ( "+" "-" "." "?" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:strand ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 29 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; + sh:in ( "+" "-" "." "?" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:genome_build ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 11 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 16 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:start_interbase_coordinate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 23 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:id ] ; + sh:targetClass biolink:GenomicSequenceLocalization . + +biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "The relationship to the disease" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . - -biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "E.g. is pathogenic for" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . + +biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 42 ; sh:path biolink:object_direction_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that genotype" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ] ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:GenotypeToDiseaseAssociation . biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Genotype ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Genotype ; sh:description "genotype that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -15433,107 +18165,116 @@ biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:object ] ; sh:targetClass biolink:GenotypeToEntityAssociationMixin . biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "the relationship type used to connect genotype to gene" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Gene ; sh:description "gene implicated in genotype" ; sh:maxCount 1 ; @@ -15541,78 +18282,58 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -15620,12 +18341,35 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:class biolink:Attribute ; @@ -15633,11 +18377,24 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ] ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:GenotypeToGeneAssociation . biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; @@ -15645,540 +18402,588 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Genotype ; - sh:description "child genotype" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:GenotypeToGenotypePartAssociation . - -biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Genotype ; + sh:description "child genotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; + sh:order 37 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:GenotypeToGenotypePartAssociation . + +biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 45 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:double ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:qualified_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_supporting_studies ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "the relationship type used to connect genotype to gene" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -16187,131 +18992,203 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ] ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ] ; sh:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; + sh:property [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -16319,153 +19196,172 @@ biolink:GenotypicSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ] ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ] ; sh:targetClass biolink:GenotypicSex . biolink:GeographicExposure a sh:NodeShape ; sh:closed true ; sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ] ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:GeographicExposure . biolink:GeographicLocation a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; + sh:ignoredProperties ( biolink:timepoint rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -16474,290 +19370,390 @@ biolink:GeographicLocation a sh:NodeShape ; [ sh:datatype xsd:float ; sh:description "latitude" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:latitude ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:longitude ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:float ; + sh:description "longitude" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:longitude ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:GeographicLocation . biolink:GeographicLocationAtTime a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates, for a particular time" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:longitude ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:float ; + sh:description "longitude" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:longitude ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], [ sh:datatype xsd:float ; sh:description "latitude" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:latitude ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ] ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:GeographicLocationAtTime . biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ] ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:GrossAnatomicalStructure . biolink:Haplotype a sh:NodeShape ; sh:closed true ; sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Haplotype . biolink:Hospitalization a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ] ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; @@ -16771,324 +19767,394 @@ biolink:Human a sh:NodeShape ; sh:description "A member of the the species Homo sapiens." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Human . biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:closed true ; sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ] ; sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . biolink:Invertebrate a sh:NodeShape ; sh:closed true ; sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ] ; sh:targetClass biolink:Invertebrate . @@ -17097,365 +20163,378 @@ biolink:JournalArticle a sh:NodeShape ; sh:closed true ; sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:creation_date ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 10 ; - sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 7 ; - sh:path biolink:keywords ], + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:license ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:category ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:pages ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 5 ; - sh:path biolink:pages ], + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:issue ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:volume ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 21 ; sh:path rdf:type ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path dct:type ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ], - [ sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:issue ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:mesh_terms ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:rights ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:format ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:summary ], + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 15 ; - sh:path biolink:provided_by ] ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:iri ] ; sh:targetClass biolink:JournalArticle . biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a log odds ratio analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ] ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:LogOddsAnalysisResult . biolink:MacromolecularComplex a sh:NodeShape ; sh:closed true ; sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ] ; sh:targetClass biolink:MacromolecularComplex . biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], [ sh:class biolink:BiologicalProcess ; sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; @@ -17463,197 +20542,326 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ] ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ] ; sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:CellularComponent ; sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; @@ -17661,88 +20869,81 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ] ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ] ; sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; @@ -17750,140 +20951,185 @@ biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; sh:description "an association which has a macromolecular machine mixin as a subject" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -17891,63 +21137,46 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; @@ -17955,80 +21184,104 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ] ; sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . biolink:Mammal a sh:NodeShape ; sh:closed true ; sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ] ; sh:targetClass biolink:Mammal . @@ -18048,31 +21301,18 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -18080,37 +21320,32 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; @@ -18119,231 +21354,257 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "derivation relationship" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:NamedThing ; + sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:description "derivation relationship" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; - sh:targetClass biolink:MaterialSampleDerivationAssociation . - -biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a material sample and a disease or phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:MaterialSampleDerivationAssociation . + +biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a material sample and a disease or phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -18351,113 +21612,167 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ] ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An association between a material sample and something." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; @@ -18470,135 +21785,139 @@ biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; biolink:MicroRNA a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ] ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The relationship to the disease" ; + sh:property [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:NamedThing ; - sh:description "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:ModelToDiseaseAssociationMixin . biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:closed true ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -18607,320 +21926,278 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ] ; - sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . - -biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; + sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . + +biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -18928,55 +22205,52 @@ biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . - -biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; @@ -18987,47 +22261,80 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -19036,105 +22343,168 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . + +biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Pathway ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; @@ -19144,110 +22514,189 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:MolecularActivityToPathwayAssociation . biolink:MolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; + [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ] ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ] ; sh:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; @@ -19260,420 +22709,514 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:property [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 36 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 39 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 11 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 38 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 6 ; + sh:path biolink:object_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:population_context_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_aspect_qualifier ] ; + sh:path biolink:population_context_qualifier ] ; sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . biolink:NoncodingRNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ] ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:NoncodingRNAProduct . biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:closed true ; sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:NucleicAcidSequenceMotif . biolink:NucleosomeModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ] ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ] ; sh:targetClass biolink:NucleosomeModification . biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; @@ -19682,70 +23225,92 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:format ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ] ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:Occurrent a sh:NodeShape ; @@ -19758,43 +23323,21 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:closed true ; sh:description "describes a characteristic of an organismal entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -19802,29 +23345,69 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:class biolink:NamedThing ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:OrganismAttribute . biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; @@ -19838,227 +23421,278 @@ biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OrganismTaxon ; sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:OrganismTaxonToEntityAssociation . biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:NamedThing ; - sh:description "the environment in which the organism occurs" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "predicate describing the relationship between the taxon and the environment" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "the environment in which the organism occurs" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:closed false ; sh:description "A relationship between two organism taxon nodes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:ignoredProperties ( biolink:associated_environmental_context rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -20066,43 +23700,81 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; @@ -20111,283 +23783,315 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:associated_environmental_context ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "the environment in which the two taxa interact" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:associated_environmental_context ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -20395,98 +24099,119 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . + +biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; + sh:closed true ; + sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 17 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; - sh:path biolink:id ], + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . - -biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; - sh:closed true ; - sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OrganismTaxon ; sh:description "the more general taxon" ; sh:maxCount 1 ; @@ -20494,400 +24219,400 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "the more specific taxon" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more specific taxon" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; + sh:order 37 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:IndividualOrganism ; + sh:property [ sh:class biolink:IndividualOrganism ; sh:description "An association between two individual organisms." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:IndividualOrganism ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:IndividualOrganism ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:OrganismToOrganismAssociation . biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; @@ -20898,72 +24623,122 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OrganismalEntity ; + sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; @@ -20972,93 +24747,86 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OrganismalEntity ; - sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -21066,256 +24834,286 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ] ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ] ; sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:ignoredProperties ( rdf:type biolink:interacting_molecules_category ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "interaction relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "interaction relationship type" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:PairwiseGeneToGeneInteraction . biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction at the molecular level between two physical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; @@ -21324,46 +25122,55 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], [ sh:class biolink:MolecularEntity ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -21372,100 +25179,99 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:order 3 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "interaction relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], [ sh:class biolink:MolecularEntity ; sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -21473,109 +25279,162 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "interaction relationship type" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ] ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ] ; sh:targetClass biolink:PairwiseMolecularInteraction . biolink:Patent a sh:NodeShape ; sh:closed true ; sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:property [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ] ; + sh:path biolink:id ] ; sh:targetClass biolink:Patent . biolink:PathognomonicityQuantifier a sh:NodeShape ; @@ -21589,76 +25448,96 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "a point in time" ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ] ; sh:targetClass biolink:PathologicalAnatomicalExposure . biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; @@ -21671,64 +25550,84 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:path rdf:type ] ; sh:targetClass biolink:PathologicalAnatomicalStructure . biolink:PathologicalEntityMixin a sh:NodeShape ; @@ -21741,126 +25640,173 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:PathologicalProcess . biolink:PathologicalProcessExposure a sh:NodeShape ; sh:closed true ; sh:description "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -21869,28 +25815,21 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:order 2 ; sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; @@ -21904,231 +25843,248 @@ biolink:Phenomenon a sh:NodeShape ; sh:description "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Phenomenon . biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "a point in time" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -22136,218 +26092,354 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 49 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 46 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ] ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:property [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 11 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path rdf:object ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_percentage ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:has_count ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:has_quotient ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_total ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path rdf:object ] ; + sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . + +biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . - -biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -22356,268 +26448,247 @@ biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 3 ; sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ] ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ] ; sh:targetClass biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . biolink:PhenotypicQuality a sh:NodeShape ; sh:closed true ; sh:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ] ; sh:targetClass biolink:PhenotypicQuality . biolink:PhenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -22625,25 +26696,24 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -22652,35 +26722,47 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:synonym ] ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ] ; sh:targetClass biolink:PhenotypicSex . biolink:PhysicalEssence a sh:NodeShape ; @@ -22698,377 +26780,397 @@ biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; biolink:PhysiologicalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + sh:order 2 ; + sh:path biolink:has_output ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ] ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:PhysiologicalProcess . biolink:PlanetaryEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists at the level of the whole planet" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:ignoredProperties ( biolink:timepoint rdf:type biolink:latitude biolink:longitude ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:PlanetaryEntity . biolink:Plant a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Plant . biolink:Polypeptide a sh:NodeShape ; sh:closed true ; sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Polypeptide . biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a two populations" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the object of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that form the subject of the association" ; sh:maxCount 1 ; @@ -23076,245 +27178,381 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the object of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ] ; sh:targetClass biolink:PopulationToPopulationAssociation . biolink:PosttranslationalModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:PosttranslationalModification . - -biolink:PreprintPublication a sh:NodeShape ; - sh:closed true ; - sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:summary ], + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; + sh:targetClass biolink:PosttranslationalModification . + +biolink:PreprintPublication a sh:NodeShape ; + sh:closed true ; + sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ] ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ] ; sh:targetClass biolink:PreprintPublication . biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; @@ -23322,92 +27560,134 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:BiologicalProcess ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:BiologicalProcess ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -23415,497 +27695,628 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:BiologicalProcess ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ] ; sh:targetClass biolink:ProcessRegulatesProcessAssociation . biolink:ProcessedMaterial a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:id ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; sh:path biolink:available_from ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:is_toxic ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ] ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ] ; sh:targetClass biolink:ProcessedMaterial . biolink:Protein a sh:NodeShape ; sh:closed true ; sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:Protein . biolink:ProteinDomain a sh:NodeShape ; sh:closed true ; sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:property [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ] ; + sh:path biolink:id ] ; sh:targetClass biolink:ProteinDomain . biolink:ProteinFamily a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ] ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ProteinFamily . biolink:ProteinIsoform a sh:NodeShape ; sh:closed true ; sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ProteinIsoform . biolink:RNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], [ sh:class biolink:Attribute ; @@ -23913,33 +28324,12 @@ biolink:RNAProduct a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ] ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:RNAProduct . biolink:RNAProductIsoform a sh:NodeShape ; @@ -23947,216 +28337,309 @@ biolink:RNAProductIsoform a sh:NodeShape ; sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:RNAProductIsoform . biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:stoichiometry ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], [ sh:description "the side of a reaction being modeled (ie: left or right)" ; sh:in ( "left" "right" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:reaction_side ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; sh:path dct:description ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; @@ -24164,413 +28647,446 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 5 ; sh:path rdf:object ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 40 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:path biolink:has_attribute ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:order 1 ; + sh:path biolink:reaction_direction ], [ sh:description "the side of a reaction being modeled (ie: left or right)" ; sh:in ( "left" "right" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:reaction_side ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:stoichiometry ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:stoichiometry ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:knowledge_level ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ] ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ReactionToParticipantAssociation . biolink:ReagentTargetedGene a sh:NodeShape ; sh:closed true ; sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ] ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ReagentTargetedGene . biolink:RegulatoryRegion a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ] ; sh:targetClass biolink:RegulatoryRegion . biolink:RelationshipQuantifier a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; + sh:ignoredProperties ( biolink:has_total biolink:has_count biolink:has_quotient rdf:type biolink:has_percentage ) ; sh:targetClass biolink:RelationshipQuantifier . biolink:RelationshipType a sh:NodeShape ; @@ -24581,6 +29097,7 @@ biolink:RelationshipType a sh:NodeShape ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ] ; sh:targetClass biolink:RelationshipType . @@ -24590,71 +29107,93 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:description "A result of a relative frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:rights ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:RelativeFrequencyAnalysisResult . biolink:SensitivityQuantifier a sh:NodeShape ; @@ -24665,162 +29204,46 @@ biolink:SensitivityQuantifier a sh:NodeShape ; biolink:SequenceAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:ignoredProperties ( biolink:phase biolink:genome_build biolink:strand biolink:start_interbase_coordinate rdf:type biolink:end_interbase_coordinate ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -24828,334 +29251,467 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; - sh:targetClass biolink:SequenceAssociation . - -biolink:SequenceFeatureRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "For example, a particular exon is part of a particular transcript or gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NucleicAcidEntity ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:SequenceAssociation . + +biolink:SequenceFeatureRelationship a sh:NodeShape ; + sh:closed true ; + sh:description "For example, a particular exon is part of a particular transcript or gene" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:SequenceFeatureRelationship . - -biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:SequenceFeatureRelationship . + +biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], [ sh:class biolink:Treatment ; @@ -25165,271 +29721,360 @@ biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:SequenceVariant ; + sh:description "variant that modulates the treatment of some disease" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ] ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . biolink:Serial a sh:NodeShape ; sh:closed true ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:iso_abbreviation ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:issue ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 16 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:issue ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 7 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:iri ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:authors ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:volume ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:rights ] ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:format ] ; sh:targetClass biolink:Serial . biolink:SeverityValue a sh:NodeShape ; sh:closed true ; sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -25437,281 +30082,374 @@ biolink:SeverityValue a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:full_name ] ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:SeverityValue . biolink:SiRNA a sh:NodeShape ; sh:closed true ; sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; sh:closed true ; sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:trade_name ], - [ sh:description "" ; + sh:property [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 2 ; sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + sh:description "" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:has_chemical_role ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_metabolite ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ] ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:id ] ; sh:targetClass biolink:SmallMolecule . biolink:Snv a sh:NodeShape ; sh:closed true ; sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:description "The state of the sequence w.r.t a reference sequence" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:synonym ] ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ] ; sh:targetClass biolink:Snv . biolink:SocioeconomicExposure a sh:NodeShape ; sh:closed true ; sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:SocioeconomicAttribute ; sh:description "connects any entity to an attribute" ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], [ sh:class biolink:OntologyClass ; @@ -25721,28 +30459,52 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ] ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:SocioeconomicExposure . biolink:SocioeconomicOutcome a sh:NodeShape ; @@ -25760,303 +30522,375 @@ biolink:StudyPopulation a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group as participants in a research study." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:StudyPopulation . biolink:StudyResult a sh:NodeShape ; sh:closed false ; sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:StudyResult . biolink:StudyVariable a sh:NodeShape ; sh:closed true ; sh:description "a variable that is used as a measure in the investigation of a study" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ] ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ] ; sh:targetClass biolink:StudyVariable . -biolink:SubjectOfInvestigation a sh:NodeShape ; - sh:closed false ; - sh:description "An entity that has the role of being studied in an investigation, study, or experiment" ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SubjectOfInvestigation . - -biolink:TaxonToTaxonAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OrganismTaxon ; +biolink:SubjectOfInvestigation a sh:NodeShape ; + sh:closed false ; + sh:description "An entity that has the role of being studied in an investigation, study, or experiment" ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:SubjectOfInvestigation . + +biolink:TaxonToTaxonAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "An association between individuals of different taxa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; @@ -26065,12 +30899,59 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -26079,540 +30960,600 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "a point in time" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ] ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:TaxonToTaxonAssociation . biolink:TextMiningResult a sh:NodeShape ; sh:closed true ; sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:rights ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ] ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:TextMiningResult . biolink:ThingWithTaxon a sh:NodeShape ; sh:closed false ; sh:description "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:ThingWithTaxon . biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:closed true ; sh:description "A gene is a collection of transcripts" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Transcript ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Transcript ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:TranscriptToGeneRelationship . biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ] ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ] ; sh:targetClass biolink:TranscriptionFactorBindingSite . biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "The relationship to the disease" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; @@ -26624,24 +31565,87 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 40 ; sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:SequenceVariant ; sh:description "A variant that has a role in modeling the disease." ; sh:maxCount 1 ; @@ -26649,331 +31653,329 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:path biolink:object_aspect_qualifier ] ; + sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . + +biolink:VariantToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ] ; - sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . - -biolink:VariantToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "E.g. is pathogenic for" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ] ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:VariantToDiseaseAssociation . biolink:VariantToEntityAssociationMixin a sh:NodeShape ; @@ -26986,63 +31988,103 @@ biolink:VariantToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:VariantToEntityAssociationMixin . biolink:VariantToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; - sh:ignoredProperties ( rdf:type ) ; + sh:ignoredProperties ( biolink:stage_qualifier biolink:quantifier_qualifier biolink:expression_site rdf:type biolink:phenotypic_state ) ; sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], [ sh:class biolink:RetrievalSource ; @@ -27050,40 +32092,43 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; @@ -27091,77 +32136,88 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -27170,128 +32226,162 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ] ; + sh:targetClass biolink:VariantToGeneAssociation . + +biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; - sh:targetClass biolink:VariantToGeneAssociation . - -biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 6 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], [ sh:class biolink:RetrievalSource ; @@ -27302,371 +32392,384 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:phenotypic_state ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 41 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ] ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:stage_qualifier ] ; sh:targetClass biolink:VariantToGeneExpressionAssociation . biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:qualified_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 49 ; sh:path biolink:frequency_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], [ sh:datatype xsd:double ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_quotient ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 40 ; sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; @@ -27678,57 +32781,126 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:integer ; - sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:description "number all populations that carry a particular allele, aka allele number" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; - sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_total ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:has_quotient ], + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:id ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 39 ; - sh:path rdf:type ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path dct:description ], [ sh:class biolink:PopulationOfIndividualOrganisms ; sh:description "the population that is observed to have the frequency" ; sh:maxCount 1 ; @@ -27736,110 +32908,90 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:integer ; - sh:description "number all populations that carry a particular allele, aka allele number" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_total ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:datatype xsd:integer ; + sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 17 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:has_percentage ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], [ sh:class biolink:SequenceVariant ; sh:description "an allele that has a certain frequency in a given population" ; sh:maxCount 1 ; @@ -27847,54 +32999,41 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 38 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:double ; + sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 36 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:has_quotient ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:VariantToPopulationAssociation . biolink:Vertebrate a sh:NodeShape ; @@ -27902,17 +33041,37 @@ biolink:Vertebrate a sh:NodeShape ; sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], [ sh:class biolink:Attribute ; @@ -27920,411 +33079,519 @@ biolink:Vertebrate a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:Vertebrate . biolink:Virus a sh:NodeShape ; sh:closed true ; sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:id ] ; sh:targetClass biolink:Virus . biolink:WebPage a sh:NodeShape ; sh:closed true ; sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:description "mesh terms tagging a publication" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:rights ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ] ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ] ; sh:targetClass biolink:WebPage . biolink:Behavior a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ] ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Behavior . biolink:BehavioralFeature a sh:NodeShape ; sh:closed true ; sh:description "A phenotypic feature which is behavioral in nature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:BehavioralFeature . biolink:CellularComponent a sh:NodeShape ; sh:closed true ; sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ] ; sh:targetClass biolink:CellularComponent . @@ -28333,648 +33600,836 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a human-readable description of an entity" ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ClinicalAttribute . + +biolink:Dataset a sh:NodeShape ; + sh:closed true ; + sh:description "an item that refers to a collection of data from a data source." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:ClinicalAttribute . - -biolink:Dataset a sh:NodeShape ; - sh:closed true ; - sh:description "an item that refers to a collection of data from a data source." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:format ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Dataset . biolink:DatasetDistribution a sh:NodeShape ; sh:closed true ; sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:distribution_download_url ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:rights ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:distribution_download_url ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:format ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:license ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ] ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:DatasetDistribution . biolink:Device a sh:NodeShape ; sh:closed true ; sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:full_name ] ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ] ; sh:targetClass biolink:Device . biolink:Exon a sh:NodeShape ; sh:closed true ; sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Exon . biolink:GeneFamily a sh:NodeShape ; sh:closed true ; sh:description "any grouping of multiple genes or gene products related by common descent" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:GeneFamily . biolink:GeneProductMixin a sh:NodeShape ; sh:closed false ; sh:description "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdfs:label ] ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:GeneProductMixin . biolink:GeneticInheritance a sh:NodeShape ; sh:closed true ; sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:path dct:description ] ; sh:targetClass biolink:GeneticInheritance . biolink:InformationContentEntity a sh:NodeShape ; sh:closed false ; sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:date ; + sh:ignoredProperties ( dct:type biolink:resource_id biolink:summary rdf:type biolink:authors biolink:upstream_resource_ids biolink:mesh_terms biolink:pages biolink:keywords biolink:distribution_download_url biolink:chapter biolink:resource_role biolink:issue dct:distribution biolink:ingest_date biolink:volume biolink:iso_abbreviation biolink:has_dataset biolink:published_in biolink:source_web_page schema1:logo ) ; + sh:property [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ] ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:InformationContentEntity . biolink:Onset a sh:NodeShape ; sh:closed true ; sh:description "The age group in which (disease) symptom manifestations appear." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:Onset . biolink:OrganismalEntity a sh:NodeShape ; sh:closed false ; sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], [ sh:class biolink:Attribute ; @@ -28982,49 +34437,68 @@ biolink:OrganismalEntity a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:OrganismalEntity . biolink:PredicateMapping a sh:NodeShape ; @@ -29032,237 +34506,288 @@ biolink:PredicateMapping a sh:NodeShape ; sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ], - [ sh:datatype xsd:string ; - sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], - [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:string ; sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:subject_derivative_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:exact_match ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 17 ; + sh:path biolink:species_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:object_part_qualifier ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:mapped_predicate ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:narrow_match ], [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:object_part_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:subject_part_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:exact_match ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:broad_match ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:subject_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:species_context_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:narrow_match ], + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:object_context_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:object_derivative_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:object_derivative_qualifier ] ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualified_predicate ] ; sh:targetClass biolink:PredicateMapping . biolink:Procedure a sh:NodeShape ; sh:closed true ; sh:description "A series of actions conducted in a certain order or manner" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ] ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Procedure . biolink:SocioeconomicAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a socioeconomic manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:SocioeconomicAttribute . biolink:TaxonomicRank a sh:NodeShape ; @@ -29273,6 +34798,7 @@ biolink:TaxonomicRank a sh:NodeShape ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ] ; sh:targetClass biolink:TaxonomicRank . @@ -29281,157 +34807,245 @@ biolink:Treatment a sh:NodeShape ; sh:closed true ; sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:Device ; + sh:description "connects an entity to one or more (medical) devices" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_device ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_procedure ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Device ; - sh:description "connects an entity to one or more (medical) devices" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_device ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:class biolink:Drug ; sh:description "connects an entity to one or more drugs" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_drug ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:has_drug ] ; + sh:targetClass biolink:Treatment . + +biolink:Zygosity a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 12 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; sh:path rdfs:label ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:timepoint ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; - sh:path biolink:has_procedure ], + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Treatment . - -biolink:Zygosity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ] ; + sh:targetClass biolink:Zygosity . + +biolink:Case a sh:NodeShape ; + sh:closed true ; + sh:description "An individual (human) organism that has a patient role in some clinical context." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Zygosity . - -biolink:Case a sh:NodeShape ; - sh:closed true ; - sh:description "An individual (human) organism that has a patient role in some clinical context." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; @@ -29439,52 +35053,22 @@ biolink:Case a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:path biolink:category ] ; sh:targetClass biolink:Case . biolink:CellLine a sh:NodeShape ; @@ -29495,121 +35079,161 @@ biolink:CellLine a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ] ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:CellLine . biolink:IndividualOrganism a sh:NodeShape ; sh:closed true ; sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ] ; sh:targetClass biolink:IndividualOrganism . @@ -29624,207 +35248,237 @@ biolink:Transcript a sh:NodeShape ; sh:closed true ; sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:Transcript . + +biolink:BiologicalProcess a sh:NodeShape ; + sh:closed true ; + sh:description "One or more causally connected executions of molecular functions" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Transcript . - -biolink:BiologicalProcess a sh:NodeShape ; - sh:closed true ; - sh:description "One or more causally connected executions of molecular functions" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PhysicalEntity ; + [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:BiologicalProcess . biolink:Drug a sh:NodeShape ; sh:closed true ; sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 4 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:is_supplement ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_chemical_role ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:iri ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; @@ -29832,47 +35486,82 @@ biolink:Drug a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 6 ; sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ] ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:is_supplement ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 4 ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:trade_name ] ; sh:targetClass biolink:Drug . biolink:ExposureEvent a sh:NodeShape ; sh:closed false ; sh:description "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:id ] ; sh:targetClass biolink:ExposureEvent . @@ -29881,195 +35570,253 @@ biolink:MaterialSample a sh:NodeShape ; sh:closed true ; sh:description "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ] ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:MaterialSample . biolink:Pathway a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ] ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Pathway . biolink:LifeStage a sh:NodeShape ; sh:closed true ; sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ] ; sh:targetClass biolink:LifeStage . @@ -30079,237 +35826,303 @@ biolink:NucleicAcidEntity a sh:NodeShape ; sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:is_metabolite ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:trade_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ] ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:NucleicAcidEntity . biolink:MolecularActivity a sh:NodeShape ; sh:closed true ; sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the input for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "The gene product, gene, or complex that catalyzes the reaction" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the input for the reaction" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], [ sh:class biolink:MolecularEntity ; sh:description "A chemical entity that is the output for the reaction" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:MolecularActivity . biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:closed true ; sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . @@ -30317,9 +36130,11 @@ biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; biolink:MacromolecularMachineMixin a sh:NodeShape ; sh:closed false ; sh:description "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:ignoredProperties ( biolink:synonym rdf:type biolink:xref ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ] ; sh:targetClass biolink:MacromolecularMachineMixin . @@ -30327,140 +36142,180 @@ biolink:MacromolecularMachineMixin a sh:NodeShape ; biolink:MolecularEntity a sh:NodeShape ; sh:closed true ; sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:ignoredProperties ( biolink:in_taxon_label biolink:has_biological_sequence biolink:in_taxon rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:is_toxic ], [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:trade_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 2 ; sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_metabolite ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path dct:description ] ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ] ; sh:targetClass biolink:MolecularEntity . biolink:PhysicalEntity a sh:NodeShape ; sh:closed true ; sh:description "An entity that has material reality (a.k.a. physical essence)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ] ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:PhysicalEntity . biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; @@ -30472,771 +36327,998 @@ biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; biolink:Genotype a sh:NodeShape ; sh:closed true ; sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Zygosity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_zygosity ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:id ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:class biolink:Zygosity ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ] ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ] ; sh:targetClass biolink:Genotype . biolink:SequenceVariant a sh:NodeShape ; sh:closed true ; sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The state of the sequence w.r.t a reference sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:Gene ; sh:description "Each allele can be associated with any number of genes" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "The state of the sequence w.r.t a reference sequence" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:SequenceVariant . biolink:ChemicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:ignoredProperties ( biolink:is_supplement biolink:highest_FDA_approval_status biolink:in_taxon_label biolink:in_taxon biolink:is_metabolite biolink:has_biological_sequence biolink:routes_of_delivery rdf:type biolink:drug_regulatory_status_world_wide ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:trade_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ] ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ChemicalEntity . biolink:Agent a sh:NodeShape ; sh:closed true ; sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:address ], - [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; - sh:order 0 ; - sh:path biolink:affiliation ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:address ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:affiliation ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ] ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:Agent . biolink:PhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:PhenotypicFeature . biolink:ChemicalRole a sh:NodeShape ; sh:closed true ; sh:description "A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:path biolink:full_name ] ; sh:targetClass biolink:ChemicalRole . biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeature . biolink:Gene a sh:NodeShape ; sh:closed true ; sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Symbol for a particular thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:symbol ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ] ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ] ; sh:targetClass biolink:Gene . biolink:Disease a sh:NodeShape ; sh:closed true ; sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Disease . biolink:BiologicalSex a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path rdf:type ] ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:BiologicalSex . biolink:AnatomicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A subcellular location, cell type or gross anatomical part" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:AnatomicalEntity . biolink:GeneOrGeneProduct a sh:NodeShape ; sh:closed false ; sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:ignoredProperties ( biolink:synonym rdf:type biolink:xref ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ] ; sh:targetClass biolink:GeneOrGeneProduct . @@ -31245,440 +37327,573 @@ biolink:QuantityValue a sh:NodeShape ; sh:closed true ; sh:description "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; + sh:property [ sh:datatype ; + sh:description "connects a quantity value to a unit" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_unit ], + [ sh:datatype xsd:double ; sh:description "connects a quantity value to a number" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:has_numeric_value ], - [ sh:description "connects a quantity value to a unit" ; + sh:path biolink:has_numeric_value ] ; + sh:targetClass biolink:QuantityValue . + +biolink:OrganismTaxon a sh:NodeShape ; + sh:closed true ; + sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:class biolink:TaxonomicRank ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_unit ] ; - sh:targetClass biolink:QuantityValue . - -biolink:OrganismTaxon a sh:NodeShape ; - sh:closed true ; - sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:path biolink:has_taxonomic_rank ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:TaxonomicRank ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_taxonomic_rank ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:order 8 ; - sh:path rdf:type ] ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:OrganismTaxon . biolink:NamedThing a sh:NodeShape ; sh:closed true ; sh:description "a databased entity or concept/class" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:ignoredProperties ( biolink:highest_FDA_approval_status dct:type biolink:resource_id biolink:timepoint rdf:type biolink:summary biolink:authors biolink:has_gene biolink:upstream_resource_ids biolink:has_procedure biolink:available_from biolink:has_zygosity biolink:has_drug biolink:has_qualitative_value biolink:has_input biolink:routes_of_delivery biolink:keywords biolink:in_taxon biolink:has_taxonomic_rank biolink:is_metabolite biolink:has_output biolink:drug_regulatory_status_world_wide biolink:ingest_date biolink:creation_date biolink:address biolink:iso_abbreviation biolink:has_dataset biolink:published_in biolink:latitude schema1:logo biolink:trade_name biolink:has_gene_or_gene_product biolink:is_toxic biolink:has_attribute_type biolink:license biolink:rights biolink:max_tolerated_dose biolink:has_chemical_role biolink:is_supplement biolink:has_device biolink:has_quantitative_value biolink:format biolink:mesh_terms biolink:pages biolink:distribution_download_url biolink:enabled_by biolink:chapter biolink:symbol biolink:resource_role biolink:has_biological_sequence biolink:issue dct:distribution biolink:in_taxon_label biolink:volume biolink:source_web_page biolink:affiliation biolink:longitude ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:NamedThing . biolink:EvidenceType a sh:NodeShape ; sh:closed true ; sh:description "Class of evidence that supports an association" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ] ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:EvidenceType . biolink:Publication a sh:NodeShape ; sh:closed true ; sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; - sh:ignoredProperties ( rdf:type ) ; + sh:ignoredProperties ( biolink:volume biolink:chapter biolink:iso_abbreviation biolink:published_in rdf:type biolink:issue ) ; sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:keywords ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; + sh:path biolink:authors ] ; + sh:targetClass biolink:Publication . + +biolink:RetrievalSource a sh:NodeShape ; + sh:closed true ; + sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], - [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 17 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ] ; - sh:targetClass biolink:Publication . - -biolink:RetrievalSource a sh:NodeShape ; - sh:closed true ; - sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:creation_date ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:anyURI ; + sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:resource_id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:upstream_resource_ids ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:format ], [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:resource_role ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:resource_id ], - [ sh:datatype xsd:string ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:rights ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:RetrievalSource . biolink:Study a sh:NodeShape ; sh:closed true ; sh:description "a detailed investigation and/or analysis" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ] ; sh:targetClass biolink:Study . @@ -31686,84 +37901,103 @@ biolink:Study a sh:NodeShape ; biolink:Attribute a sh:NodeShape ; sh:closed true ; sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; + sh:ignoredProperties ( biolink:in_taxon_label biolink:in_taxon biolink:has_biological_sequence biolink:timepoint rdf:type biolink:has_gene_or_gene_product ) ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; sh:closed false ; sh:description "a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type." ; - sh:ignoredProperties ( rdf:type ) ; + sh:ignoredProperties ( biolink:timepoint rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ] ; sh:targetClass biolink:OntologyClass . diff --git a/project/shex/biolink_model.shex b/project/shex/biolink_model.shex index 7d11ef096..acaa3bc6b 100644 --- a/project/shex/biolink_model.shex +++ b/project/shex/biolink_model.shex @@ -1,3 +1,5 @@ +# metamodel_version: 1.7.0 +# version: 4.2.4 BASE PREFIX rdf: PREFIX rdfs: @@ -4329,4 +4331,3 @@ linkml:Sparqlpath xsd:string ) } - diff --git a/src/biolink_model/datamodel/model.py b/src/biolink_model/datamodel/model.py index b0a40f1f4..c2cb10092 100644 --- a/src/biolink_model/datamodel/model.py +++ b/src/biolink_model/datamodel/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink_model.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-10-10T17:39:00 +# Generation date: 2024-10-10T16:38:06 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -11,7 +11,7 @@ from jsonasobj2 import JsonObj, as_dict from typing import Optional, List, Union, Dict, ClassVar, Any from dataclasses import dataclass -from datetime import date, datetime +from datetime import date, datetime, time from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions from linkml_runtime.utils.slot import Slot @@ -1383,7 +1383,7 @@ class OrganismTaxonToEnvironmentAssociationId(AssociationId): pass -@dataclass +@dataclass(repr=False) class MappingCollection(YAMLRoot): """ A collection of deprecated mappings. @@ -1405,7 +1405,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class PredicateMapping(YAMLRoot): """ A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should @@ -1512,7 +1512,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class OntologyClass(YAMLRoot): """ a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be @@ -1550,7 +1550,7 @@ class Annotation(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.Annotation -@dataclass +@dataclass(repr=False) class QuantityValue(Annotation): """ A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric @@ -1616,7 +1616,7 @@ class PathognomonicityQuantifier(SpecificityQuantifier): class_model_uri: ClassVar[URIRef] = BIOLINK.PathognomonicityQuantifier -@dataclass +@dataclass(repr=False) class FrequencyQuantifier(RelationshipQuantifier): _inherited_slots: ClassVar[List[str]] = [] @@ -1655,7 +1655,7 @@ class ChemicalOrDrugOrTreatment(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalOrDrugOrTreatment -@dataclass +@dataclass(repr=False) class Entity(YAMLRoot): """ Root Biolink Model class for all things and informational relationships, real or imagined. @@ -1734,7 +1734,7 @@ def __new__(cls, *args, **kwargs): -@dataclass +@dataclass(repr=False) class NamedThing(Entity): """ a databased entity or concept/class @@ -1813,7 +1813,7 @@ def __new__(cls, *args, **kwargs): -@dataclass +@dataclass(repr=False) class Attribute(NamedThing): """ A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, @@ -1866,7 +1866,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalRole(Attribute): """ A role played by the molecular entity or part thereof within a chemical context. @@ -1896,7 +1896,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BiologicalSex(Attribute): _inherited_slots: ClassVar[List[str]] = [] @@ -1923,7 +1923,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PhenotypicSex(BiologicalSex): """ An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. @@ -1953,7 +1953,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypicSex(BiologicalSex): """ An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex @@ -1984,7 +1984,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SeverityValue(Attribute): """ describes the severity of a phenotypic feature or disease @@ -2014,7 +2014,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RelationshipType(OntologyClass): """ An OWL property used as an edge label @@ -2037,7 +2037,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class TaxonomicRank(OntologyClass): """ A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom) @@ -2060,7 +2060,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class OrganismTaxon(NamedThing): """ A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). @@ -2094,7 +2094,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Event(NamedThing): """ Something that happens at a given place and time. @@ -2123,7 +2123,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AdministrativeEntity(NamedThing): _inherited_slots: ClassVar[List[str]] = [] @@ -2145,7 +2145,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Agent(AdministrativeEntity): """ person, group, organization or project that provides a piece of information (i.e. a knowledge association) @@ -2187,7 +2187,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class InformationContentEntity(NamedThing): """ a piece of information that typically describes some topic of discourse or is used as support. @@ -2227,7 +2227,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class StudyResult(InformationContentEntity): """ A collection of data items from a study that are about a particular study subject or experimental unit (the @@ -2254,7 +2254,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class StudyVariable(InformationContentEntity): """ a variable that is used as a measure in the investigation of a study @@ -2283,7 +2283,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CommonDataElement(InformationContentEntity): """ A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable @@ -2314,7 +2314,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ConceptCountAnalysisResult(StudyResult): """ A result of a concept count analysis. @@ -2343,7 +2343,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ObservedExpectedFrequencyAnalysisResult(StudyResult): """ A result of a observed expected frequency analysis. @@ -2372,7 +2372,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RelativeFrequencyAnalysisResult(StudyResult): """ A result of a relative frequency analysis. @@ -2401,7 +2401,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class TextMiningResult(StudyResult): """ A result of text mining. @@ -2430,7 +2430,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChiSquaredAnalysisResult(StudyResult): """ A result of a chi squared analysis. @@ -2459,7 +2459,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class LogOddsAnalysisResult(StudyResult): """ A result of a log odds ratio analysis. @@ -2488,7 +2488,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Dataset(InformationContentEntity): """ an item that refers to a collection of data from a data source. @@ -2517,7 +2517,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DatasetDistribution(InformationContentEntity): """ an item that holds distribution level information about a dataset. @@ -2550,7 +2550,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DatasetVersion(InformationContentEntity): """ an item that holds version level information about a dataset. @@ -2591,7 +2591,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DatasetSummary(InformationContentEntity): """ an item that holds summary level information about a dataset. @@ -2628,7 +2628,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ConfidenceLevel(InformationContentEntity): """ Level of confidence in a statement @@ -2657,7 +2657,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EvidenceType(InformationContentEntity): """ Class of evidence that supports an association @@ -2686,7 +2686,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Publication(InformationContentEntity): """ Any ‘published’ piece of information. Publications are considered broadly to include any document or document part @@ -2759,7 +2759,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Book(Publication): """ This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. @@ -2794,7 +2794,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BookChapter(Publication): _inherited_slots: ClassVar[List[str]] = [] @@ -2835,7 +2835,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Serial(Publication): """ This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. @@ -2882,7 +2882,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Article(Publication): """ a piece of writing on a particular topic presented as a stand-alone section of a larger publication @@ -2930,7 +2930,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class JournalArticle(Article): """ an article, typically presenting results of research, that is published in an issue of a scientific journal. @@ -2961,7 +2961,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Patent(Publication): """ a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use @@ -2992,7 +2992,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class WebPage(Publication): """ a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, @@ -3023,7 +3023,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PreprintPublication(Publication): """ a document reresenting an early version of an author's original scholarly work, such as a research paper or a @@ -3054,7 +3054,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DrugLabel(Publication): """ a document accompanying a drug or its container that provides written, printed or graphic information about the @@ -3086,7 +3086,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RetrievalSource(InformationContentEntity): """ Provides information about how a particular InformationResource served as a source from which knowledge expressed @@ -3161,7 +3161,7 @@ class PhysicalEssence(PhysicalEssenceOrOccurrent): class_model_uri: ClassVar[URIRef] = BIOLINK.PhysicalEssence -@dataclass +@dataclass(repr=False) class PhysicalEntity(NamedThing): """ An entity that has material reality (a.k.a. physical essence). @@ -3214,7 +3214,7 @@ class ActivityAndBehavior(Occurrent): class_model_uri: ClassVar[URIRef] = BIOLINK.ActivityAndBehavior -@dataclass +@dataclass(repr=False) class Activity(NamedThing): """ An activity is something that occurs over a period of time and acts upon or with entities; it may include @@ -3244,7 +3244,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Study(Activity): """ a detailed investigation and/or analysis @@ -3273,7 +3273,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Procedure(NamedThing): """ A series of actions conducted in a certain order or manner @@ -3302,7 +3302,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Phenomenon(NamedThing): """ a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question @@ -3331,7 +3331,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Device(NamedThing): """ A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment @@ -3360,7 +3360,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiagnosticAid(NamedThing): """ A device or substance used to help diagnose disease or injury @@ -3401,7 +3401,7 @@ class SubjectOfInvestigation(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.SubjectOfInvestigation -@dataclass +@dataclass(repr=False) class MaterialSample(PhysicalEntity): """ A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a @@ -3432,7 +3432,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PlanetaryEntity(NamedThing): """ Any entity or process that exists at the level of the whole planet @@ -3461,7 +3461,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EnvironmentalProcess(PlanetaryEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -3487,7 +3487,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EnvironmentalFeature(PlanetaryEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -3513,7 +3513,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeographicLocation(PlanetaryEntity): """ a location that can be described in lat/long coordinates @@ -3550,7 +3550,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeographicLocationAtTime(GeographicLocation): """ a location that can be described in lat/long coordinates, for a particular time @@ -3583,7 +3583,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ThingWithTaxon(YAMLRoot): """ A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; @@ -3610,7 +3610,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class BiologicalEntity(NamedThing): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -3640,7 +3640,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenomicEntity(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -3658,7 +3658,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class EpigenomicEntity(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -3676,7 +3676,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class ChemicalEntity(NamedThing): """ A chemical entity is a physical entity that pertains to chemistry or biochemistry. @@ -3727,7 +3727,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularEntity(ChemicalEntity): """ A molecular entity is a chemical entity composed of individual or covalently bonded atoms. @@ -3760,7 +3760,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SmallMolecule(MolecularEntity): """ A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, @@ -3792,7 +3792,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalMixture(ChemicalEntity): """ A chemical mixture is a chemical entity composed of two or more molecular entities. @@ -3838,7 +3838,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class NucleicAcidEntity(MolecularEntity): """ A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based @@ -3882,7 +3882,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RegulatoryRegion(BiologicalEntity): """ A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- @@ -3916,7 +3916,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AccessibleDnaRegion(RegulatoryRegion): """ A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as @@ -3950,7 +3950,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class TranscriptionFactorBindingSite(RegulatoryRegion): """ A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that @@ -3984,7 +3984,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularMixture(ChemicalMixture): """ A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and @@ -4014,7 +4014,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ComplexMolecularMixture(ChemicalMixture): """ A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown @@ -4044,7 +4044,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BiologicalProcessOrActivity(BiologicalEntity): """ Either an individual molecular activity, or a collection of causally connected molecular activities in a @@ -4089,7 +4089,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularActivity(BiologicalProcessOrActivity): """ An execution of a molecular function carried out by a gene product or macromolecular complex. @@ -4133,7 +4133,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BiologicalProcess(BiologicalProcessOrActivity): """ One or more causally connected executions of molecular functions @@ -4162,7 +4162,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Pathway(BiologicalProcess): _inherited_slots: ClassVar[List[str]] = ["in_taxon", "has_input", "has_output", "enabled_by"] @@ -4188,7 +4188,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PhysiologicalProcess(BiologicalProcess): _inherited_slots: ClassVar[List[str]] = ["in_taxon", "has_input", "has_output", "enabled_by"] @@ -4214,7 +4214,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Behavior(BiologicalProcess): _inherited_slots: ClassVar[List[str]] = ["in_taxon", "has_input", "has_output", "enabled_by"] @@ -4240,7 +4240,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ProcessedMaterial(ChemicalMixture): """ A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a @@ -4270,7 +4270,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Drug(MolecularMixture): """ A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease @@ -4299,7 +4299,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EnvironmentalFoodContaminant(ChemicalEntity): _inherited_slots: ClassVar[List[str]] = ["has_chemical_role"] @@ -4325,7 +4325,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class FoodAdditive(ChemicalEntity): _inherited_slots: ClassVar[List[str]] = ["has_chemical_role"] @@ -4351,7 +4351,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Food(ChemicalMixture): """ A substance consumed by a living organism as a source of nutrition @@ -4380,7 +4380,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismAttribute(Attribute): """ describes a characteristic of an organismal entity. @@ -4410,7 +4410,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PhenotypicQuality(OrganismAttribute): """ A property of a phenotype @@ -4440,7 +4440,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneticInheritance(BiologicalEntity): """ The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, @@ -4470,7 +4470,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismalEntity(BiologicalEntity): """ A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding @@ -4500,7 +4500,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Bacterium(OrganismalEntity): """ A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and @@ -4530,7 +4530,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Virus(OrganismalEntity): """ A virus is a microorganism that replicates itself as a microRNA and infects the host cell. @@ -4559,7 +4559,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CellularOrganism(OrganismalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -4585,7 +4585,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Mammal(CellularOrganism): """ A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the @@ -4615,7 +4615,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Human(Mammal): """ A member of the the species Homo sapiens. @@ -4644,7 +4644,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Plant(CellularOrganism): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -4670,7 +4670,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Invertebrate(CellularOrganism): """ An animal lacking a vertebral column. This group consists of 98% of all animal species. @@ -4699,7 +4699,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Vertebrate(CellularOrganism): """ A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column. @@ -4728,7 +4728,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Fungus(CellularOrganism): """ A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, @@ -4759,7 +4759,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class LifeStage(OrganismalEntity): """ A stage of development or growth of an organism, including post-natal adult stages @@ -4788,7 +4788,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class IndividualOrganism(OrganismalEntity): """ An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: @@ -4818,7 +4818,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PopulationOfIndividualOrganisms(OrganismalEntity): """ A collection of individuals from the same taxonomic class distinguished by one or more characteristics. @@ -4848,7 +4848,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class StudyPopulation(PopulationOfIndividualOrganisms): """ A group of people banded together or treated as a group as participants in a research study. @@ -4877,7 +4877,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiseaseOrPhenotypicFeature(BiologicalEntity): """ Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these @@ -4909,7 +4909,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Disease(DiseaseOrPhenotypicFeature): """ A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that @@ -4940,7 +4940,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PhenotypicFeature(DiseaseOrPhenotypicFeature): """ A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an @@ -4970,7 +4970,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BehavioralFeature(PhenotypicFeature): """ A phenotypic feature which is behavioral in nature. @@ -4999,7 +4999,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AnatomicalEntity(OrganismalEntity): """ A subcellular location, cell type or gross anatomical part @@ -5028,7 +5028,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CellularComponent(AnatomicalEntity): """ A location in or around a cell @@ -5057,7 +5057,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Cell(AnatomicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5083,7 +5083,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CellLine(OrganismalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5109,7 +5109,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GrossAnatomicalStructure(AnatomicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5161,7 +5161,7 @@ class ChemicalEntityOrProteinOrPolypeptide(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalEntityOrProteinOrPolypeptide -@dataclass +@dataclass(repr=False) class MacromolecularMachineMixin(YAMLRoot): """ A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. @@ -5195,7 +5195,7 @@ class GeneOrGeneProduct(MacromolecularMachineMixin): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneOrGeneProduct -@dataclass +@dataclass(repr=False) class Gene(BiologicalEntity): """ A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A @@ -5242,7 +5242,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneProductMixin(GeneOrGeneProduct): """ The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA @@ -5284,7 +5284,7 @@ class GeneProductIsoformMixin(GeneProductMixin): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneProductIsoformMixin -@dataclass +@dataclass(repr=False) class MacromolecularComplex(BiologicalEntity): """ A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which @@ -5318,7 +5318,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class NucleosomeModification(BiologicalEntity): """ A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a @@ -5366,7 +5366,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Genome(BiologicalEntity): """ A genome is the sum of genetic material within a cell or virion. @@ -5399,7 +5399,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Exon(BiologicalEntity): """ A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA @@ -5429,7 +5429,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Transcript(BiologicalEntity): """ An RNA synthesized on a DNA or RNA template by an RNA polymerase. @@ -5458,7 +5458,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CodingSequence(BiologicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5488,7 +5488,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Polypeptide(BiologicalEntity): """ A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based @@ -5519,7 +5519,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Protein(Polypeptide): """ A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated @@ -5563,7 +5563,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ProteinIsoform(Protein): """ Represents a protein that is a specific isoform of the canonical or reference protein. See @@ -5607,7 +5607,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ProteinDomain(BiologicalEntity): """ A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently @@ -5643,7 +5643,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PosttranslationalModification(BiologicalEntity): """ A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to @@ -5687,7 +5687,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ProteinFamily(BiologicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5718,7 +5718,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class NucleicAcidSequenceMotif(BiologicalEntity): """ A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological @@ -5748,7 +5748,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RNAProduct(Transcript): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5788,7 +5788,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RNAProductIsoform(RNAProduct): """ Represents a protein that is a specific isoform of the canonical or reference RNA @@ -5831,7 +5831,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class NoncodingRNAProduct(RNAProduct): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5857,7 +5857,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MicroRNA(NoncodingRNAProduct): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5883,7 +5883,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SiRNA(NoncodingRNAProduct): """ A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular @@ -5914,7 +5914,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneGroupingMixin(YAMLRoot): """ any grouping of multiple genes or gene products @@ -5936,7 +5936,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GeneFamily(BiologicalEntity): """ any grouping of multiple genes or gene products related by common descent @@ -5970,7 +5970,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Zygosity(Attribute): _inherited_slots: ClassVar[List[str]] = [] @@ -5997,7 +5997,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Genotype(BiologicalEntity): """ An information content entity that describes a genome by specifying the total variation in genomic sequence and/or @@ -6035,7 +6035,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Haplotype(BiologicalEntity): """ A set of zero or more Alleles on a single instance of a Sequence[VMC] @@ -6068,7 +6068,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SequenceVariant(BiologicalEntity): """ A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. @@ -6106,7 +6106,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Snv(SequenceVariant): """ SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist @@ -6135,7 +6135,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ReagentTargetedGene(BiologicalEntity): """ A gene altered in its expression level in the context of some experiment as a result of being targeted by @@ -6169,7 +6169,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalAttribute(Attribute): """ Attributes relating to a clinical manifestation @@ -6199,7 +6199,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalMeasurement(ClinicalAttribute): """ A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject @@ -6235,7 +6235,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalModifier(ClinicalAttribute): """ Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, @@ -6266,7 +6266,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalCourse(ClinicalAttribute): """ The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the @@ -6297,7 +6297,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Onset(ClinicalCourse): """ The age group in which (disease) symptom manifestations appear. @@ -6327,7 +6327,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalEntity(NamedThing): """ Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed @@ -6357,7 +6357,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalTrial(ClinicalEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -6383,7 +6383,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalIntervention(ClinicalEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -6409,7 +6409,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalFinding(PhenotypicFeature): """ this category is currently considered broad enough to tag clinical lab measurements and other biological @@ -6444,7 +6444,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Hospitalization(ClinicalIntervention): _inherited_slots: ClassVar[List[str]] = [] @@ -6470,7 +6470,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SocioeconomicAttribute(Attribute): """ Attributes relating to a socioeconomic manifestation @@ -6500,7 +6500,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Case(IndividualOrganism): """ An individual (human) organism that has a patient role in some clinical context. @@ -6529,7 +6529,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Cohort(StudyPopulation): """ A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a @@ -6559,7 +6559,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ExposureEvent(OntologyClass): """ A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more @@ -6582,7 +6582,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GenomicBackgroundExposure(Attribute): """ A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or @@ -6648,7 +6648,7 @@ class PathologicalEntityMixin(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.PathologicalEntityMixin -@dataclass +@dataclass(repr=False) class PathologicalProcess(BiologicalProcess): """ A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, @@ -6678,7 +6678,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PathologicalProcessExposure(Attribute): """ A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an @@ -6713,7 +6713,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PathologicalAnatomicalStructure(AnatomicalEntity): """ An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, @@ -6743,7 +6743,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PathologicalAnatomicalExposure(Attribute): """ An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or @@ -6778,7 +6778,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiseaseOrPhenotypicFeatureExposure(Attribute): """ A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or @@ -6814,7 +6814,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalExposure(Attribute): """ A chemical exposure is an intake of a particular chemical entity. @@ -6853,7 +6853,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ComplexChemicalExposure(Attribute): """ A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. @@ -6883,7 +6883,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DrugExposure(ChemicalExposure): """ A drug exposure is an intake of a particular drug. @@ -6917,7 +6917,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DrugToGeneInteractionExposure(DrugExposure): """ drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are @@ -6953,7 +6953,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Treatment(NamedThing): """ A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices @@ -7002,7 +7002,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BioticExposure(Attribute): """ An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). @@ -7036,7 +7036,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EnvironmentalExposure(Attribute): """ A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), @@ -7071,7 +7071,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeographicExposure(EnvironmentalExposure): """ A geographic exposure is a factor relating to geographic proximity to some impactful entity. @@ -7105,7 +7105,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BehavioralExposure(Attribute): """ A behavioral exposure is a factor relating to behavior impacting an individual. @@ -7139,7 +7139,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SocioeconomicExposure(Attribute): """ A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. @@ -7293,7 +7293,7 @@ class SocioeconomicOutcome(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.SocioeconomicOutcome -@dataclass +@dataclass(repr=False) class Association(Entity): """ A typed association between two entities, supported by evidence @@ -7309,8 +7309,8 @@ class Association(Entity): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None negated: Optional[Union[bool, Bool]] = None qualifier: Optional[str] = None qualifiers: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() @@ -7500,7 +7500,7 @@ def __new__(cls, *args, **kwargs): -@dataclass +@dataclass(repr=False) class ChemicalEntityAssessesNamedThingAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -7510,11 +7510,11 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalEntityAssessesNamedThingAssociation id: Union[str, ChemicalEntityAssessesNamedThingAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ChemicalEntityId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7543,7 +7543,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ContributorAssociation(Association): """ Any association between an entity (such as a publication) and various agents that contribute to its realisation @@ -7556,11 +7556,11 @@ class ContributorAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ContributorAssociation id: Union[str, ContributorAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, InformationContentEntityId] = None predicate: Union[str, PredicateType] = None object: Union[str, AgentId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" qualifiers: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -7594,7 +7594,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypeToGenotypePartAssociation(Association): """ Any association between one genotype and a genotypic entity that is a sub-component of it @@ -7607,11 +7607,11 @@ class GenotypeToGenotypePartAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypeToGenotypePartAssociation id: Union[str, GenotypeToGenotypePartAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None object: Union[str, GenotypeId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7640,7 +7640,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypeToGeneAssociation(Association): """ Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single @@ -7654,11 +7654,11 @@ class GenotypeToGeneAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypeToGeneAssociation id: Union[str, GenotypeToGeneAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None object: Union[str, GeneId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7687,7 +7687,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypeToVariantAssociation(Association): """ Any association between a genotype and a sequence variant. @@ -7700,11 +7700,11 @@ class GenotypeToVariantAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypeToVariantAssociation id: Union[str, GenotypeToVariantAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None object: Union[str, SequenceVariantId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7733,7 +7733,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToGeneAssociation(Association): """ abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes @@ -7748,10 +7748,10 @@ class GeneToGeneAssociation(Association): id: Union[str, GeneToGeneAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): @@ -7770,7 +7770,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToGeneHomologyAssociation(GeneToGeneAssociation): """ A homology association between two genes. May be orthology (in which case the species of subject and object should @@ -7784,11 +7784,11 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToGeneHomologyAssociation id: Union[str, GeneToGeneHomologyAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7817,7 +7817,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToGeneFamilyAssociation(Association): """ Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence @@ -7832,11 +7832,11 @@ class GeneToGeneFamilyAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToGeneFamilyAssociation id: Union[str, GeneToGeneFamilyAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, GeneId] = None object: Union[str, GeneFamilyId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7865,7 +7865,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneExpressionMixin(YAMLRoot): """ Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the @@ -7899,7 +7899,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GeneToGeneCoexpressionAssociation(GeneToGeneAssociation): """ Indicates that two genes are co-expressed, generally under the same conditions. @@ -7912,11 +7912,11 @@ class GeneToGeneCoexpressionAssociation(GeneToGeneAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToGeneCoexpressionAssociation id: Union[str, GeneToGeneCoexpressionAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" quantifier_qualifier: Optional[Union[str, OntologyClassId]] = None expression_site: Optional[Union[str, AnatomicalEntityId]] = None stage_qualifier: Optional[Union[str, LifeStageId]] = None @@ -7951,7 +7951,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): """ An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between @@ -7965,11 +7965,11 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.PairwiseGeneToGeneInteraction id: Union[str, PairwiseGeneToGeneInteractionId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7988,7 +7988,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): """ An interaction at the molecular level between two physical entities @@ -8001,11 +8001,11 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): class_model_uri: ClassVar[URIRef] = BIOLINK.PairwiseMolecularInteraction id: Union[str, PairwiseMolecularInteractionId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, MolecularEntityId] = None predicate: Union[str, PredicateType] = None object: Union[str, MolecularEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" interacting_molecules_category: Optional[Union[str, OntologyClassId]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8038,7 +8038,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CellLineToEntityAssociationMixin(YAMLRoot): """ An relationship between a cell line and another entity @@ -8073,7 +8073,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class CellLineToDiseaseOrPhenotypicFeatureAssociation(Association): """ An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an @@ -8089,9 +8089,9 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(Association): id: Union[str, CellLineToDiseaseOrPhenotypicFeatureAssociationId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, DiseaseOrPhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8120,7 +8120,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalEntityToEntityAssociationMixin(YAMLRoot): """ An interaction between a chemical entity and another entity @@ -8155,7 +8155,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DrugToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): """ An interaction between a drug and another entity @@ -8195,7 +8195,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class ChemicalToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): """ An interaction between a chemical entity and another entity @@ -8235,7 +8235,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class CaseToEntityAssociationMixin(YAMLRoot): """ An abstract association for use where the case is the subject @@ -8270,7 +8270,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class ChemicalToChemicalAssociation(Association): """ A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal @@ -8284,11 +8284,11 @@ class ChemicalToChemicalAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalToChemicalAssociation id: Union[str, ChemicalToChemicalAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, ChemicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8317,7 +8317,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -8327,11 +8327,11 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.ReactionToParticipantAssociation id: Union[str, ReactionToParticipantAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None object: Union[str, ChemicalEntityId] = None subject: Union[str, MolecularEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" stoichiometry: Optional[int] = None reaction_direction: Optional[Union[str, "ReactionDirectionEnum"]] = None reaction_side: Optional[Union[str, "ReactionSideEnum"]] = None @@ -8362,7 +8362,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ReactionToCatalystAssociation(ReactionToParticipantAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -8372,11 +8372,11 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.ReactionToCatalystAssociation id: Union[str, ReactionToCatalystAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[str, MolecularEntityId] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8395,7 +8395,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): """ A causal relationship between two chemical entities, where the subject represents the upstream entity and the @@ -8410,11 +8410,11 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalToChemicalDerivationAssociation id: Union[str, ChemicalToChemicalDerivationAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ChemicalEntityId] = None object: Union[str, ChemicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" catalyst_qualifier: Optional[Union[Union[dict, MacromolecularMachineMixin], List[Union[dict, MacromolecularMachineMixin]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8448,7 +8448,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalToDiseaseOrPhenotypicFeatureAssociation(Association): """ An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise @@ -8464,9 +8464,9 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(Association): id: Union[str, ChemicalToDiseaseOrPhenotypicFeatureAssociationId] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[str, DiseaseOrPhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8495,7 +8495,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(Association): """ This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic @@ -8511,9 +8511,9 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(Associati id: Union[str, ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociationId] = None subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" FDA_adverse_event_level: Optional[Union[str, "FDAIDAAdverseEventEnum"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8546,7 +8546,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation): """ This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic @@ -8562,9 +8562,9 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C id: Union[str, ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociationId] = None subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8593,7 +8593,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToPathwayAssociation(Association): """ An interaction between a gene or gene product and a biological process or pathway. @@ -8607,10 +8607,10 @@ class GeneToPathwayAssociation(Association): id: Union[str, GeneToPathwayAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, PathwayId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8639,7 +8639,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularActivityToPathwayAssociation(Association): """ Association that holds the relationship between a reaction and the pathway it participates in. @@ -8652,11 +8652,11 @@ class MolecularActivityToPathwayAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.MolecularActivityToPathwayAssociation id: Union[str, MolecularActivityToPathwayAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, MolecularActivityId] = None object: Union[str, PathwayId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8685,7 +8685,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalToPathwayAssociation(Association): """ An interaction between a chemical entity and a biological process or pathway. @@ -8699,10 +8699,10 @@ class ChemicalToPathwayAssociation(Association): id: Union[str, ChemicalToPathwayAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ChemicalEntityId] = None object: Union[str, PathwayId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8731,7 +8731,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -8741,11 +8741,11 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.NamedThingAssociatedWithLikelihoodOfNamedThingAssociation id: Union[str, NamedThingAssociatedWithLikelihoodOfNamedThingAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_aspect_qualifier: Optional[str] = None subject_context_qualifier: Optional[Union[str, OntologyClassId]] = None object_aspect_qualifier: Optional[str] = None @@ -8794,7 +8794,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalGeneInteractionAssociation(Association): """ describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical @@ -8809,11 +8809,11 @@ class ChemicalGeneInteractionAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalGeneInteractionAssociation id: Union[str, ChemicalGeneInteractionAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ChemicalEntityId] = None object: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[Union[str, "ChemicalOrGeneOrGeneProductFormOrVariantEnum"]] = None subject_part_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalPartQualifierEnum"]] = None subject_derivative_qualifier: Optional[Union[str, "ChemicalEntityDerivativeEnum"]] = None @@ -8874,7 +8874,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneRegulatesGeneAssociation(Association): """ Describes a regulatory relationship between two genes or gene products. @@ -8887,14 +8887,14 @@ class GeneRegulatesGeneAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneRegulatesGeneAssociation id: Union[str, GeneRegulatesGeneAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object_aspect_qualifier: Union[str, "GeneOrGeneProductOrChemicalEntityAspectEnum"] = None object_direction_qualifier: Union[str, "DirectionQualifierEnum"] = None qualified_predicate: str = None subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" species_context_qualifier: Optional[Union[str, OrganismTaxonId]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8942,7 +8942,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ProcessRegulatesProcessAssociation(Association): """ Describes a regulatory relationship between two genes or gene products. @@ -8955,11 +8955,11 @@ class ProcessRegulatesProcessAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ProcessRegulatesProcessAssociation id: Union[str, ProcessRegulatesProcessAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, BiologicalProcessId] = None predicate: Union[str, PredicateType] = None object: Union[str, BiologicalProcessId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8988,7 +8988,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalAffectsGeneAssociation(Association): """ Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, @@ -9002,11 +9002,11 @@ class ChemicalAffectsGeneAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalAffectsGeneAssociation id: Union[str, ChemicalAffectsGeneAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ChemicalEntityId] = None predicate: Union[str, PredicateType] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[Union[str, "ChemicalOrGeneOrGeneProductFormOrVariantEnum"]] = None subject_part_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalPartQualifierEnum"]] = None subject_derivative_qualifier: Optional[Union[str, "ChemicalEntityDerivativeEnum"]] = None @@ -9095,7 +9095,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneAffectsChemicalAssociation(Association): """ Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, @@ -9109,11 +9109,11 @@ class GeneAffectsChemicalAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneAffectsChemicalAssociation id: Union[str, GeneAffectsChemicalAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None object: Union[str, ChemicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[Union[str, "ChemicalOrGeneOrGeneProductFormOrVariantEnum"]] = None subject_part_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalPartQualifierEnum"]] = None subject_derivative_qualifier: Optional[str] = None @@ -9206,7 +9206,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DrugToGeneAssociation(Association): """ An interaction between a drug and a gene or gene product. @@ -9221,9 +9221,9 @@ class DrugToGeneAssociation(Association): id: Union[str, DrugToGeneAssociationId] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9252,7 +9252,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MaterialSampleToEntityAssociationMixin(YAMLRoot): """ An association between a material sample and something. @@ -9287,7 +9287,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class MaterialSampleDerivationAssociation(Association): """ An association between a material sample and the material entity from which it is derived. @@ -9300,11 +9300,11 @@ class MaterialSampleDerivationAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.MaterialSampleDerivationAssociation id: Union[str, MaterialSampleDerivationAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, MaterialSampleId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9333,7 +9333,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(Association): """ An association between a material sample and a disease or phenotype. @@ -9349,8 +9349,8 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9379,7 +9379,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiseaseToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -9411,7 +9411,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class EntityToExposureEventAssociationMixin(YAMLRoot): """ An association between some entity and an exposure event. @@ -9446,7 +9446,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DiseaseToExposureEventAssociation(Association): """ An association between an exposure event and a disease. @@ -9462,8 +9462,8 @@ class DiseaseToExposureEventAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9492,7 +9492,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EntityToOutcomeAssociationMixin(YAMLRoot): """ An association between some entity and an outcome @@ -9527,7 +9527,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class ExposureEventToOutcomeAssociation(Association): """ An association between an exposure event and an outcome. @@ -9543,8 +9543,8 @@ class ExposureEventToOutcomeAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None population_context_qualifier: Optional[Union[str, PopulationOfIndividualOrganismsId]] = None temporal_context_qualifier: Optional[Union[str, TimeType]] = None @@ -9581,7 +9581,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class FrequencyQualifierMixin(YAMLRoot): """ Qualifier for frequency type associations @@ -9620,7 +9620,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class EntityToFeatureOrDiseaseQualifiersMixin(FrequencyQualifierMixin): """ Qualifiers for entity to disease or phenotype associations. @@ -9660,7 +9660,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class FeatureOrDiseaseQualifiersToEntityMixin(FrequencyQualifierMixin): """ Qualifiers for disease or phenotype to entity associations. @@ -9700,7 +9700,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class EntityToPhenotypicFeatureAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin): _inherited_slots: ClassVar[List[str]] = [] @@ -9752,7 +9752,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class PhenotypicFeatureToEntityAssociationMixin(FeatureOrDiseaseQualifiersToEntityMixin): _inherited_slots: ClassVar[List[str]] = [] @@ -9794,7 +9794,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class PhenotypicFeatureToPhenotypicFeatureAssociation(Association): """ Association between two concept nodes of phenotypic character, qualified by the predicate used. This association @@ -9811,8 +9811,8 @@ class PhenotypicFeatureToPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -9869,7 +9869,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class InformationContentEntityToNamedThingAssociation(Association): """ association between a named thing and a information content entity where the specific context of the relationship @@ -9887,11 +9887,11 @@ class InformationContentEntityToNamedThingAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.InformationContentEntityToNamedThingAssociation id: Union[str, InformationContentEntityToNamedThingAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9920,7 +9920,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EntityToDiseaseAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin): """ mixin class for any association whose object (target node) is a disease @@ -9945,7 +9945,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DiseaseOrPhenotypicFeatureToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -9977,7 +9977,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DiseaseOrPhenotypicFeatureToLocationAssociation(Association): """ An association between either a disease or a phenotypic feature and an anatomical entity, where the @@ -9993,9 +9993,9 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(Association): id: Union[str, DiseaseOrPhenotypicFeatureToLocationAssociationId] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[str, AnatomicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10024,7 +10024,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(Association): """ An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance. @@ -10038,10 +10038,10 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(Association): id: Union[str, DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociationId] = None subject: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None object: Union[str, GeneticInheritanceId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10070,7 +10070,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EntityToDiseaseOrPhenotypicFeatureAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10102,7 +10102,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GenotypeToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10134,7 +10134,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GenotypeToPhenotypicFeatureAssociation(Association): """ Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, @@ -10149,10 +10149,10 @@ class GenotypeToPhenotypicFeatureAssociation(Association): id: Union[str, GenotypeToPhenotypicFeatureAssociationId] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10209,7 +10209,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ExposureEventToPhenotypicFeatureAssociation(Association): """ Any association between an environment and a phenotypic feature, where being in the environment influences the @@ -10225,9 +10225,9 @@ class ExposureEventToPhenotypicFeatureAssociation(Association): id: Union[str, ExposureEventToPhenotypicFeatureAssociationId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ExposureEventId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10284,7 +10284,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiseaseToPhenotypicFeatureAssociation(Association): """ An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the @@ -10299,10 +10299,10 @@ class DiseaseToPhenotypicFeatureAssociation(Association): id: Union[str, DiseaseToPhenotypicFeatureAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, DiseaseId] = None object: Union[str, PhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" onset_qualifier: Optional[Union[str, OnsetId]] = None has_count: Optional[int] = None has_total: Optional[int] = None @@ -10379,7 +10379,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CaseToPhenotypicFeatureAssociation(Association): """ An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or @@ -10396,8 +10396,8 @@ class CaseToPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10454,7 +10454,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BehaviorToBehavioralFeatureAssociation(Association): """ An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has @@ -10469,10 +10469,10 @@ class BehaviorToBehavioralFeatureAssociation(Association): id: Union[str, BehaviorToBehavioralFeatureAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, BehaviorId] = None object: Union[str, BehavioralFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10529,7 +10529,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10561,7 +10561,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class VariantToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10593,7 +10593,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GeneToDiseaseOrPhenotypicFeatureAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -10603,11 +10603,11 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToDiseaseOrPhenotypicFeatureAssociation id: Union[str, GeneToDiseaseOrPhenotypicFeatureAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseOrPhenotypicFeatureId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_aspect_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalEntityAspectEnum"]] = None object_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None frequency_qualifier: Optional[Union[str, FrequencyValue]] = None @@ -10664,7 +10664,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10674,11 +10674,11 @@ class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssocia class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToPhenotypicFeatureAssociation id: Union[str, GeneToPhenotypicFeatureAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, PhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10722,7 +10722,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10732,11 +10732,11 @@ class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToDiseaseAssociation id: Union[str, GeneToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10776,7 +10776,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10786,11 +10786,11 @@ class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.CausalGeneToDiseaseAssociation id: Union[str, CausalGeneToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10830,7 +10830,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10840,11 +10840,11 @@ class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.CorrelatedGeneToDiseaseAssociation id: Union[str, CorrelatedGeneToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10884,7 +10884,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10894,11 +10894,11 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.DruggableGeneToDiseaseAssociation id: Union[str, DruggableGeneToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[str, DiseaseId] = None subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10943,7 +10943,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PhenotypicFeatureToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -10955,9 +10955,9 @@ class PhenotypicFeatureToDiseaseAssociation(Association): id: Union[str, PhenotypicFeatureToDiseaseAssociationId] = None subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11014,7 +11014,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantToGeneAssociation(Association): """ An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in @@ -11029,10 +11029,10 @@ class VariantToGeneAssociation(Association): id: Union[str, VariantToGeneAssociationId] = None subject: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[str, GeneId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11061,7 +11061,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantToGeneExpressionAssociation(VariantToGeneAssociation): """ An association between a variant and expression of a gene (i.e. e-QTL) @@ -11075,10 +11075,10 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation): id: Union[str, VariantToGeneExpressionAssociationId] = None subject: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[str, GeneId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" quantifier_qualifier: Optional[Union[str, OntologyClassId]] = None expression_site: Optional[Union[str, AnatomicalEntityId]] = None stage_qualifier: Optional[Union[str, LifeStageId]] = None @@ -11113,7 +11113,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantToPopulationAssociation(Association): """ An association between a variant and a population, where the variant has particular frequency in the population @@ -11127,10 +11127,10 @@ class VariantToPopulationAssociation(Association): id: Union[str, VariantToPopulationAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, SequenceVariantId] = None object: Union[str, PopulationOfIndividualOrganismsId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" has_quotient: Optional[float] = None has_count: Optional[int] = None has_total: Optional[int] = None @@ -11179,7 +11179,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PopulationToPopulationAssociation(Association): """ An association between a two populations @@ -11192,11 +11192,11 @@ class PopulationToPopulationAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.PopulationToPopulationAssociation id: Union[str, PopulationToPopulationAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, PopulationOfIndividualOrganismsId] = None object: Union[str, PopulationOfIndividualOrganismsId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11225,7 +11225,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantToPhenotypicFeatureAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11237,9 +11237,9 @@ class VariantToPhenotypicFeatureAssociation(Association): id: Union[str, VariantToPhenotypicFeatureAssociationId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, SequenceVariantId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11296,7 +11296,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11306,11 +11306,11 @@ class VariantToDiseaseAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.VariantToDiseaseAssociation id: Union[str, VariantToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11363,7 +11363,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypeToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11373,11 +11373,11 @@ class GenotypeToDiseaseAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypeToDiseaseAssociation id: Union[str, GenotypeToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11430,7 +11430,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ModelToDiseaseAssociationMixin(YAMLRoot): """ This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in @@ -11467,7 +11467,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GeneAsAModelOfDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11477,11 +11477,11 @@ class GeneAsAModelOfDiseaseAssociation(GeneToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneAsAModelOfDiseaseAssociation id: Union[str, GeneAsAModelOfDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None object: Union[str, DiseaseId] = None subject: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -11516,7 +11516,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantAsAModelOfDiseaseAssociation(VariantToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11526,11 +11526,11 @@ class VariantAsAModelOfDiseaseAssociation(VariantToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.VariantAsAModelOfDiseaseAssociation id: Union[str, VariantAsAModelOfDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, SequenceVariantId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11573,7 +11573,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypeAsAModelOfDiseaseAssociation(GenotypeToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11583,11 +11583,11 @@ class GenotypeAsAModelOfDiseaseAssociation(GenotypeToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypeAsAModelOfDiseaseAssociation id: Union[str, GenotypeAsAModelOfDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, GenotypeId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11630,7 +11630,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CellLineAsAModelOfDiseaseAssociation(CellLineToDiseaseOrPhenotypicFeatureAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11642,9 +11642,9 @@ class CellLineAsAModelOfDiseaseAssociation(CellLineToDiseaseOrPhenotypicFeatureA id: Union[str, CellLineAsAModelOfDiseaseAssociationId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, CellLineId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11697,7 +11697,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismalEntityAsAModelOfDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11709,9 +11709,9 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(Association): id: Union[str, OrganismalEntityAsAModelOfDiseaseAssociationId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11764,7 +11764,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismToOrganismAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11775,10 +11775,10 @@ class OrganismToOrganismAssociation(Association): id: Union[str, OrganismToOrganismAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, IndividualOrganismId] = None object: Union[str, IndividualOrganismId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11802,7 +11802,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class TaxonToTaxonAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11813,10 +11813,10 @@ class TaxonToTaxonAssociation(Association): id: Union[str, TaxonToTaxonAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11840,7 +11840,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11850,11 +11850,11 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation class_model_uri: ClassVar[URIRef] = BIOLINK.GeneHasVariantThatContributesToDiseaseAssociation id: Union[str, GeneHasVariantThatContributesToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -11887,7 +11887,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToExpressionSiteAssociation(Association): """ An association between a gene and a gene expression site, possibly qualified by stage/timing info. @@ -11900,11 +11900,11 @@ class GeneToExpressionSiteAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToExpressionSiteAssociation id: Union[str, GeneToExpressionSiteAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, AnatomicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" stage_qualifier: Optional[Union[str, LifeStageId]] = None quantifier_qualifier: Optional[Union[str, OntologyClassId]] = None @@ -11941,7 +11941,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SequenceVariantModulatesTreatmentAssociation(Association): """ An association between a sequence variant and a treatment or health intervention. The treatment object itself @@ -11956,10 +11956,10 @@ class SequenceVariantModulatesTreatmentAssociation(Association): id: Union[str, SequenceVariantModulatesTreatmentAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, SequenceVariantId] = None object: Union[str, TreatmentId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): @@ -11978,7 +11978,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class FunctionalAssociation(Association): """ An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either @@ -11993,10 +11993,10 @@ class FunctionalAssociation(Association): id: Union[str, FunctionalAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, OntologyClassId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12020,7 +12020,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MacromolecularMachineToEntityAssociationMixin(YAMLRoot): """ an association which has a macromolecular machine mixin as a subject @@ -12055,7 +12055,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class MacromolecularMachineToMolecularActivityAssociation(FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity @@ -12071,10 +12071,10 @@ class MacromolecularMachineToMolecularActivityAssociation(FunctionalAssociation) id: Union[str, MacromolecularMachineToMolecularActivityAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, MolecularActivityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12098,7 +12098,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MacromolecularMachineToBiologicalProcessAssociation(FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a biological process @@ -12114,10 +12114,10 @@ class MacromolecularMachineToBiologicalProcessAssociation(FunctionalAssociation) id: Union[str, MacromolecularMachineToBiologicalProcessAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, BiologicalProcessId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12141,7 +12141,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MacromolecularMachineToCellularComponentAssociation(FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component @@ -12157,10 +12157,10 @@ class MacromolecularMachineToCellularComponentAssociation(FunctionalAssociation) id: Union[str, MacromolecularMachineToCellularComponentAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, CellularComponentId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12184,7 +12184,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularActivityToChemicalEntityAssociation(Association): """ Added in response to capturing relationship between microbiome activities as measured via measurements of blood @@ -12199,10 +12199,10 @@ class MolecularActivityToChemicalEntityAssociation(Association): id: Union[str, MolecularActivityToChemicalEntityAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, MolecularActivityId] = None object: Union[str, ChemicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12226,7 +12226,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularActivityToMolecularActivityAssociation(Association): """ Added in response to capturing relationship between microbiome activities as measured via measurements of blood @@ -12241,10 +12241,10 @@ class MolecularActivityToMolecularActivityAssociation(Association): id: Union[str, MolecularActivityToMolecularActivityAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, MolecularActivityId] = None object: Union[str, MolecularActivityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12268,7 +12268,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToGoTermAssociation(FunctionalAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -12279,10 +12279,10 @@ class GeneToGoTermAssociation(FunctionalAssociation): id: Union[str, GeneToGoTermAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, GeneId] = None object: Union[str, OntologyClassId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12306,7 +12306,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EntityToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -12319,8 +12319,8 @@ class EntityToDiseaseAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None clinical_approval_status: Optional[Union[str, "ClinicalApprovalStatusEnum"]] = None max_research_phase: Optional[Union[str, "ResearchPhaseEnum"]] = None @@ -12342,7 +12342,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EntityToPhenotypicFeatureAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -12355,8 +12355,8 @@ class EntityToPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None clinical_approval_status: Optional[Union[str, "ClinicalApprovalStatusEnum"]] = None max_research_phase: Optional[Union[str, "ResearchPhaseEnum"]] = None @@ -12378,7 +12378,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SequenceAssociation(Association): """ An association between a sequence feature and a nucleic acid entity it is localized to. @@ -12394,8 +12394,8 @@ class SequenceAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12409,7 +12409,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenomicSequenceLocalization(SequenceAssociation): """ A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may @@ -12423,11 +12423,11 @@ class GenomicSequenceLocalization(SequenceAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GenomicSequenceLocalization id: Union[str, GenomicSequenceLocalizationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NucleicAcidEntityId] = None object: Union[str, NucleicAcidEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" start_interbase_coordinate: Optional[int] = None end_interbase_coordinate: Optional[int] = None genome_build: Optional[Union[str, "StrandEnum"]] = None @@ -12476,7 +12476,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SequenceFeatureRelationship(Association): """ For example, a particular exon is part of a particular transcript or gene @@ -12490,10 +12490,10 @@ class SequenceFeatureRelationship(Association): id: Union[str, SequenceFeatureRelationshipId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NucleicAcidEntityId] = None object: Union[str, NucleicAcidEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12517,7 +12517,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class TranscriptToGeneRelationship(SequenceFeatureRelationship): """ A gene is a collection of transcripts @@ -12531,10 +12531,10 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): id: Union[str, TranscriptToGeneRelationshipId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, TranscriptId] = None object: Union[str, GeneId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12558,7 +12558,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToGeneProductRelationship(SequenceFeatureRelationship): """ A gene is transcribed and potentially translated to a gene product @@ -12571,11 +12571,11 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToGeneProductRelationship id: Union[str, GeneToGeneProductRelationshipId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, GeneId] = None object: Union[dict, GeneProductMixin] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12604,7 +12604,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ExonToTranscriptRelationship(SequenceFeatureRelationship): """ A transcript is formed from multiple exons @@ -12618,10 +12618,10 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): id: Union[str, ExonToTranscriptRelationshipId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ExonId] = None object: Union[str, TranscriptId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12645,7 +12645,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): """ A regulatory relationship between two genes @@ -12658,11 +12658,11 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation id: Union[str, ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[dict, ChemicalEntityOrGeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" object_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -12695,7 +12695,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AnatomicalEntityToAnatomicalEntityAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -12706,10 +12706,10 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): id: Union[str, AnatomicalEntityToAnatomicalEntityAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, AnatomicalEntityId] = None object: Union[str, AnatomicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): @@ -12728,7 +12728,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnatomicalEntityAssociation): """ A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are @@ -12743,11 +12743,11 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat class_model_uri: ClassVar[URIRef] = BIOLINK.AnatomicalEntityToAnatomicalEntityPartOfAssociation id: Union[str, AnatomicalEntityToAnatomicalEntityPartOfAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, AnatomicalEntityId] = None object: Union[str, AnatomicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12776,7 +12776,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToAnatomicalEntityAssociation): """ A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are @@ -12791,11 +12791,11 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA class_model_uri: ClassVar[URIRef] = BIOLINK.AnatomicalEntityToAnatomicalEntityOntogenicAssociation id: Union[str, AnatomicalEntityToAnatomicalEntityOntogenicAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, AnatomicalEntityId] = None object: Union[str, AnatomicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12824,7 +12824,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismTaxonToEntityAssociation(YAMLRoot): """ An association between an organism taxon and another entity @@ -12859,7 +12859,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class OrganismTaxonToOrganismTaxonAssociation(Association): """ A relationship between two organism taxon nodes @@ -12873,10 +12873,10 @@ class OrganismTaxonToOrganismTaxonAssociation(Association): id: Union[str, OrganismTaxonToOrganismTaxonAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.predicate): @@ -12900,7 +12900,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAssociation): """ A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo @@ -12913,11 +12913,11 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss class_model_uri: ClassVar[URIRef] = BIOLINK.OrganismTaxonToOrganismTaxonSpecialization id: Union[str, OrganismTaxonToOrganismTaxonSpecializationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12946,7 +12946,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssociation): """ An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and @@ -12961,11 +12961,11 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci class_model_uri: ClassVar[URIRef] = BIOLINK.OrganismTaxonToOrganismTaxonInteraction id: Union[str, OrganismTaxonToOrganismTaxonInteractionId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" associated_environmental_context: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -12998,7 +12998,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismTaxonToEnvironmentAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -13008,11 +13008,11 @@ class OrganismTaxonToEnvironmentAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.OrganismTaxonToEnvironmentAssociation id: Union[str, OrganismTaxonToEnvironmentAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): diff --git a/src/biolink_model/datamodel/pydanticmodel_v2.py b/src/biolink_model/datamodel/pydanticmodel_v2.py index 89df2655e..f7d4fcdcb 100644 --- a/src/biolink_model/datamodel/pydanticmodel_v2.py +++ b/src/biolink_model/datamodel/pydanticmodel_v2.py @@ -1,52 +1,70 @@ from __future__ import annotations + +import re +import sys from datetime import ( + date, datetime, - date + time ) from decimal import Decimal from enum import Enum -import re -import sys from typing import ( Any, + ClassVar, + Dict, List, Literal, - Dict, Optional, Union ) -from pydantic.version import VERSION as PYDANTIC_VERSION -if int(PYDANTIC_VERSION[0])>=2: - from pydantic import ( - BaseModel, - ConfigDict, - Field, - field_validator - ) -else: - from pydantic import ( - BaseModel, - Field, - validator - ) + +from pydantic import ( + BaseModel, + ConfigDict, + Field, + RootModel, + field_validator +) + metamodel_version = "None" version = "4.2.4" -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = "forbid", - arbitrary_types_allowed = True, - use_enum_values = True): +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + validate_assignment = True, + validate_default = True, + extra = "forbid", + arbitrary_types_allowed = True, + use_enum_values = True, + strict = False, + ) pass + + +class LinkMLMeta(RootModel): + root: Dict[str, Any] = {} + model_config = ConfigDict(frozen=True) + + def __getattr__(self, key:str): + return getattr(self.root, key) + + def __getitem__(self, key:str): + return self.root[key] + + def __setitem__(self, key:str, value): + self.root[key] = value + + def __contains__(self, key:str) -> bool: + return key in self.root + + +linkml_meta = None + class ApprovalStatusEnum(str, Enum): # Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments. discovery_and_development_phase = "discovery_and_development_phase" @@ -364,6 +382,7 @@ class KnowledgeLevelEnum(str, Enum): not_provided = "not_provided" + class MappingCollection(ConfiguredBaseModel): """ A collection of deprecated mappings. @@ -457,7 +476,7 @@ class Entity(ConfiguredBaseModel): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Entity","biolink:Entity"]] = Field(["biolink:Entity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -469,13 +488,13 @@ class NamedThing(Entity): a databased entity or concept/class """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NamedThing","biolink:NamedThing"]] = Field(["biolink:NamedThing"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -493,11 +512,11 @@ class Attribute(NamedThing, OntologyClass): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/Attribute","biolink:Attribute"]] = Field(["biolink:Attribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -514,11 +533,11 @@ class ChemicalRole(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalRole","biolink:ChemicalRole"]] = Field(["biolink:ChemicalRole"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -532,11 +551,11 @@ class BiologicalSex(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalSex","biolink:BiologicalSex"]] = Field(["biolink:BiologicalSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -553,11 +572,11 @@ class PhenotypicSex(BiologicalSex): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicSex","biolink:PhenotypicSex"]] = Field(["biolink:PhenotypicSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -574,11 +593,11 @@ class GenotypicSex(BiologicalSex): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypicSex","biolink:GenotypicSex"]] = Field(["biolink:GenotypicSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -595,11 +614,11 @@ class SeverityValue(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/SeverityValue","biolink:SeverityValue"]] = Field(["biolink:SeverityValue"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -625,13 +644,13 @@ class OrganismTaxon(NamedThing): """ has_taxonomic_rank: Optional[str] = Field(None) provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxon","biolink:OrganismTaxon"]] = Field(["biolink:OrganismTaxon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -643,13 +662,13 @@ class Event(NamedThing): Something that happens at a given place and time. """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Event","biolink:Event"]] = Field(["biolink:Event"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -658,13 +677,13 @@ class Event(NamedThing): class AdministrativeEntity(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AdministrativeEntity","biolink:AdministrativeEntity"]] = Field(["biolink:AdministrativeEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -675,16 +694,16 @@ class Agent(AdministrativeEntity): """ person, group, organization or project that provides a piece of information (i.e. a knowledge association) """ - affiliation: Optional[List[str]] = Field(default_factory=list, description="""a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.""") + affiliation: Optional[List[str]] = Field(None, description="""a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.""") address: Optional[str] = Field(None, description="""the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Agent","biolink:Agent"]] = Field(["biolink:Agent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -700,13 +719,13 @@ class InformationContentEntity(NamedThing): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/InformationContentEntity","biolink:InformationContentEntity"]] = Field(["biolink:InformationContentEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -722,13 +741,13 @@ class StudyResult(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyResult","biolink:StudyResult"]] = Field(["biolink:StudyResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -744,13 +763,13 @@ class StudyVariable(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyVariable","biolink:StudyVariable"]] = Field(["biolink:StudyVariable"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -766,13 +785,13 @@ class CommonDataElement(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CommonDataElement","biolink:CommonDataElement"]] = Field(["biolink:CommonDataElement"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -788,13 +807,13 @@ class ConceptCountAnalysisResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ConceptCountAnalysisResult","biolink:ConceptCountAnalysisResult"]] = Field(["biolink:ConceptCountAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -810,13 +829,13 @@ class ObservedExpectedFrequencyAnalysisResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ObservedExpectedFrequencyAnalysisResult","biolink:ObservedExpectedFrequencyAnalysisResult"]] = Field(["biolink:ObservedExpectedFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -832,13 +851,13 @@ class RelativeFrequencyAnalysisResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RelativeFrequencyAnalysisResult","biolink:RelativeFrequencyAnalysisResult"]] = Field(["biolink:RelativeFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -854,13 +873,13 @@ class TextMiningResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TextMiningResult","biolink:TextMiningResult"]] = Field(["biolink:TextMiningResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -876,13 +895,13 @@ class ChiSquaredAnalysisResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChiSquaredAnalysisResult","biolink:ChiSquaredAnalysisResult"]] = Field(["biolink:ChiSquaredAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -898,13 +917,13 @@ class LogOddsAnalysisResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/LogOddsAnalysisResult","biolink:LogOddsAnalysisResult"]] = Field(["biolink:LogOddsAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -920,13 +939,13 @@ class Dataset(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Dataset","biolink:Dataset"]] = Field(["biolink:Dataset"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -943,13 +962,13 @@ class DatasetDistribution(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetDistribution","biolink:DatasetDistribution"]] = Field(["biolink:DatasetDistribution"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -968,13 +987,13 @@ class DatasetVersion(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetVersion","biolink:DatasetVersion"]] = Field(["biolink:DatasetVersion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -992,13 +1011,13 @@ class DatasetSummary(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetSummary","biolink:DatasetSummary"]] = Field(["biolink:DatasetSummary"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1014,13 +1033,13 @@ class ConfidenceLevel(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ConfidenceLevel","biolink:ConfidenceLevel"]] = Field(["biolink:ConfidenceLevel"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1036,13 +1055,13 @@ class EvidenceType(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EvidenceType","biolink:EvidenceType"]] = Field(["biolink:EvidenceType"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1053,12 +1072,12 @@ class Publication(InformationContentEntity): """ Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1066,11 +1085,11 @@ class Publication(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Publication","biolink:Publication"]] = Field(["biolink:Publication"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1081,12 +1100,12 @@ class Book(Publication): """ This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1094,11 +1113,11 @@ class Book(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Books should have industry-standard identifier such as from ISBN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Book","biolink:Book"]] = Field(["biolink:Book"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""Should generally be set to an ontology class defined term for 'book'.""") + type: Optional[List[str]] = Field(None, description="""Should generally be set to an ontology class defined term for 'book'.""") name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1109,12 +1128,12 @@ class BookChapter(Publication): published_in: str = Field(..., description="""The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") chapter: Optional[str] = Field(None, description="""chapter of a book""") - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1122,11 +1141,11 @@ class BookChapter(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BookChapter","biolink:BookChapter"]] = Field(["biolink:BookChapter"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1140,12 +1159,12 @@ class Serial(Publication): iso_abbreviation: Optional[str] = Field(None, description="""Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1153,11 +1172,11 @@ class Serial(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Serials (journals) should have industry-standard identifier such as from ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Serial","biolink:Serial"]] = Field(["biolink:Serial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""Should generally be set to an ontology class defined term for 'serial' or 'journal'.""") + type: Optional[List[str]] = Field(None, description="""Should generally be set to an ontology class defined term for 'serial' or 'journal'.""") name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1172,12 +1191,12 @@ class Article(Publication): iso_abbreviation: Optional[str] = Field(None, description="""Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1185,11 +1204,11 @@ class Article(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Article","biolink:Article"]] = Field(["biolink:Article"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1204,12 +1223,12 @@ class JournalArticle(Article): iso_abbreviation: Optional[str] = Field(None, description="""Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1217,11 +1236,11 @@ class JournalArticle(Article): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/JournalArticle","biolink:JournalArticle"]] = Field(["biolink:JournalArticle"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1232,12 +1251,12 @@ class Patent(Publication): """ a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1245,11 +1264,11 @@ class Patent(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Patent","biolink:Patent"]] = Field(["biolink:Patent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1260,12 +1279,12 @@ class WebPage(Publication): """ a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features. """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1273,11 +1292,11 @@ class WebPage(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/WebPage","biolink:WebPage"]] = Field(["biolink:WebPage"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1288,12 +1307,12 @@ class PreprintPublication(Publication): """ a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal. """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1301,11 +1320,11 @@ class PreprintPublication(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PreprintPublication","biolink:PreprintPublication"]] = Field(["biolink:PreprintPublication"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1316,12 +1335,12 @@ class DrugLabel(Publication): """ a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc. """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1329,11 +1348,11 @@ class DrugLabel(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DrugLabel","biolink:DrugLabel"]] = Field(["biolink:DrugLabel"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1347,18 +1366,18 @@ class RetrievalSource(InformationContentEntity): resource_id: str = Field(..., description="""The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") resource_role: ResourceRoleEnum = Field(..., description="""The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge.""") upstream_resource_ids: Optional[str] = Field(None, description="""The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RetrievalSource","biolink:RetrievalSource"]] = Field(["biolink:RetrievalSource"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1384,13 +1403,13 @@ class PhysicalEntity(PhysicalEssence, NamedThing): An entity that has material reality (a.k.a. physical essence). """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhysicalEntity","biolink:PhysicalEntity"]] = Field(["biolink:PhysicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1416,13 +1435,13 @@ class Activity(ActivityAndBehavior, NamedThing): An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Activity","biolink:Activity"]] = Field(["biolink:Activity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1434,13 +1453,13 @@ class Study(Activity): a detailed investigation and/or analysis """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Study","biolink:Study"]] = Field(["biolink:Study"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1452,13 +1471,13 @@ class Procedure(ActivityAndBehavior, NamedThing): A series of actions conducted in a certain order or manner """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Procedure","biolink:Procedure"]] = Field(["biolink:Procedure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1470,13 +1489,13 @@ class Phenomenon(Occurrent, NamedThing): a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Phenomenon","biolink:Phenomenon"]] = Field(["biolink:Phenomenon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1488,13 +1507,13 @@ class Device(NamedThing): A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Device","biolink:Device"]] = Field(["biolink:Device"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1506,13 +1525,13 @@ class DiagnosticAid(NamedThing): A device or substance used to help diagnose disease or injury """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiagnosticAid","biolink:DiagnosticAid"]] = Field(["biolink:DiagnosticAid"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1531,13 +1550,13 @@ class MaterialSample(SubjectOfInvestigation, PhysicalEntity): A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO] """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MaterialSample","biolink:MaterialSample"]] = Field(["biolink:MaterialSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1549,13 +1568,13 @@ class PlanetaryEntity(NamedThing): Any entity or process that exists at the level of the whole planet """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PlanetaryEntity","biolink:PlanetaryEntity"]] = Field(["biolink:PlanetaryEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1564,13 +1583,13 @@ class PlanetaryEntity(NamedThing): class EnvironmentalProcess(PlanetaryEntity, Occurrent): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalProcess","biolink:EnvironmentalProcess"]] = Field(["biolink:EnvironmentalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1579,13 +1598,13 @@ class EnvironmentalProcess(PlanetaryEntity, Occurrent): class EnvironmentalFeature(PlanetaryEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalFeature","biolink:EnvironmentalFeature"]] = Field(["biolink:EnvironmentalFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1599,13 +1618,13 @@ class GeographicLocation(PlanetaryEntity): latitude: Optional[float] = Field(None, description="""latitude""") longitude: Optional[float] = Field(None, description="""longitude""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicLocation","biolink:GeographicLocation"]] = Field(["biolink:GeographicLocation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1620,13 +1639,13 @@ class GeographicLocationAtTime(GeographicLocation): latitude: Optional[float] = Field(None, description="""latitude""") longitude: Optional[float] = Field(None, description="""longitude""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicLocationAtTime","biolink:GeographicLocationAtTime"]] = Field(["biolink:GeographicLocationAtTime"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1645,13 +1664,13 @@ class BiologicalEntity(ThingWithTaxon, NamedThing): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalEntity","biolink:BiologicalEntity"]] = Field(["biolink:BiologicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1677,12 +1696,12 @@ class BiologicalProcessOrActivity(BiologicalEntity, Occurrent, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalProcessOrActivity","biolink:BiologicalProcessOrActivity"]] = Field(["biolink:BiologicalProcessOrActivity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1700,12 +1719,12 @@ class MolecularActivity(BiologicalProcessOrActivity, Occurrent, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivity","biolink:MolecularActivity"]] = Field(["biolink:MolecularActivity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1723,12 +1742,12 @@ class BiologicalProcess(BiologicalProcessOrActivity, Occurrent, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalProcess","biolink:BiologicalProcess"]] = Field(["biolink:BiologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1743,12 +1762,12 @@ class Pathway(BiologicalProcess, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Pathway","biolink:Pathway"]] = Field(["biolink:Pathway"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1763,12 +1782,12 @@ class PhysiologicalProcess(BiologicalProcess, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhysiologicalProcess","biolink:PhysiologicalProcess"]] = Field(["biolink:PhysiologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1783,12 +1802,12 @@ class Behavior(BiologicalProcess, ActivityAndBehavior, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Behavior","biolink:Behavior"]] = Field(["biolink:Behavior"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1806,11 +1825,11 @@ class OrganismAttribute(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismAttribute","biolink:OrganismAttribute"]] = Field(["biolink:OrganismAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -1827,11 +1846,11 @@ class PhenotypicQuality(OrganismAttribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicQuality","biolink:PhenotypicQuality"]] = Field(["biolink:PhenotypicQuality"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -1844,13 +1863,13 @@ class GeneticInheritance(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneticInheritance","biolink:GeneticInheritance"]] = Field(["biolink:GeneticInheritance"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1864,13 +1883,13 @@ class OrganismalEntity(BiologicalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismalEntity","biolink:OrganismalEntity"]] = Field(["biolink:OrganismalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1884,13 +1903,13 @@ class Bacterium(OrganismalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Bacterium","biolink:Bacterium"]] = Field(["biolink:Bacterium"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1904,13 +1923,13 @@ class Virus(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Virus","biolink:Virus"]] = Field(["biolink:Virus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1921,13 +1940,13 @@ class CellularOrganism(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellularOrganism","biolink:CellularOrganism"]] = Field(["biolink:CellularOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1941,13 +1960,13 @@ class Mammal(CellularOrganism, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Mammal","biolink:Mammal"]] = Field(["biolink:Mammal"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1961,13 +1980,13 @@ class Human(Mammal, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Human","biolink:Human"]] = Field(["biolink:Human"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1978,13 +1997,13 @@ class Plant(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Plant","biolink:Plant"]] = Field(["biolink:Plant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1998,13 +2017,13 @@ class Invertebrate(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Invertebrate","biolink:Invertebrate"]] = Field(["biolink:Invertebrate"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2018,13 +2037,13 @@ class Vertebrate(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Vertebrate","biolink:Vertebrate"]] = Field(["biolink:Vertebrate"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2038,13 +2057,13 @@ class Fungus(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Fungus","biolink:Fungus"]] = Field(["biolink:Fungus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2058,13 +2077,13 @@ class LifeStage(OrganismalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/LifeStage","biolink:LifeStage"]] = Field(["biolink:LifeStage"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2078,13 +2097,13 @@ class IndividualOrganism(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/IndividualOrganism","biolink:IndividualOrganism"]] = Field(["biolink:IndividualOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2098,13 +2117,13 @@ class PopulationOfIndividualOrganisms(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PopulationOfIndividualOrganisms","biolink:PopulationOfIndividualOrganisms"]] = Field(["biolink:PopulationOfIndividualOrganisms"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2118,13 +2137,13 @@ class StudyPopulation(PopulationOfIndividualOrganisms): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyPopulation","biolink:StudyPopulation"]] = Field(["biolink:StudyPopulation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2138,13 +2157,13 @@ class DiseaseOrPhenotypicFeature(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature","biolink:DiseaseOrPhenotypicFeature"]] = Field(["biolink:DiseaseOrPhenotypicFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2158,13 +2177,13 @@ class Disease(DiseaseOrPhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Disease","biolink:Disease"]] = Field(["biolink:Disease"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2178,13 +2197,13 @@ class PhenotypicFeature(DiseaseOrPhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicFeature","biolink:PhenotypicFeature"]] = Field(["biolink:PhenotypicFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2198,13 +2217,13 @@ class BehavioralFeature(PhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BehavioralFeature","biolink:BehavioralFeature"]] = Field(["biolink:BehavioralFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2218,13 +2237,13 @@ class AnatomicalEntity(OrganismalEntity, PhysicalEssence): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntity","biolink:AnatomicalEntity"]] = Field(["biolink:AnatomicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2238,13 +2257,13 @@ class CellularComponent(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellularComponent","biolink:CellularComponent"]] = Field(["biolink:CellularComponent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2255,13 +2274,13 @@ class Cell(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Cell","biolink:Cell"]] = Field(["biolink:Cell"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2272,13 +2291,13 @@ class CellLine(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellLine","biolink:CellLine"]] = Field(["biolink:CellLine"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2289,13 +2308,13 @@ class GrossAnatomicalStructure(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GrossAnatomicalStructure","biolink:GrossAnatomicalStructure"]] = Field(["biolink:GrossAnatomicalStructure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2318,12 +2337,12 @@ class RegulatoryRegion(ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, Biologi in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RegulatoryRegion","biolink:RegulatoryRegion"]] = Field(["biolink:RegulatoryRegion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2339,12 +2358,12 @@ class AccessibleDnaRegion(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, G in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AccessibleDnaRegion","biolink:AccessibleDnaRegion"]] = Field(["biolink:AccessibleDnaRegion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2360,12 +2379,12 @@ class TranscriptionFactorBindingSite(RegulatoryRegion, ChemicalEntityOrGeneOrGen in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TranscriptionFactorBindingSite","biolink:TranscriptionFactorBindingSite"]] = Field(["biolink:TranscriptionFactorBindingSite"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2389,13 +2408,13 @@ class ChemicalEntity(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneO is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntity","biolink:ChemicalEntity"]] = Field(["biolink:ChemicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2413,13 +2432,13 @@ class MolecularEntity(ChemicalEntity): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularEntity","biolink:MolecularEntity"]] = Field(["biolink:MolecularEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2437,13 +2456,13 @@ class SmallMolecule(MolecularEntity): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SmallMolecule","biolink:SmallMolecule"]] = Field(["biolink:SmallMolecule"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2464,13 +2483,13 @@ class ChemicalMixture(ChemicalEntity): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalMixture","biolink:ChemicalMixture"]] = Field(["biolink:ChemicalMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2492,12 +2511,12 @@ class NucleicAcidEntity(MolecularEntity, GenomicEntity, ThingWithTaxon, Physical is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleicAcidEntity","biolink:NucleicAcidEntity"]] = Field(["biolink:NucleicAcidEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2518,13 +2537,13 @@ class MolecularMixture(ChemicalMixture): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularMixture","biolink:MolecularMixture"]] = Field(["biolink:MolecularMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2545,13 +2564,13 @@ class ComplexMolecularMixture(ChemicalMixture): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ComplexMolecularMixture","biolink:ComplexMolecularMixture"]] = Field(["biolink:ComplexMolecularMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2572,13 +2591,13 @@ class ProcessedMaterial(ChemicalMixture): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProcessedMaterial","biolink:ProcessedMaterial"]] = Field(["biolink:ProcessedMaterial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2600,12 +2619,12 @@ class Drug(MolecularMixture, ChemicalOrDrugOrTreatment, OntologyClass): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Drug","biolink:Drug"]] = Field(["biolink:Drug"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2619,13 +2638,13 @@ class EnvironmentalFoodContaminant(ChemicalEntity): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalFoodContaminant","biolink:EnvironmentalFoodContaminant"]] = Field(["biolink:EnvironmentalFoodContaminant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2639,13 +2658,13 @@ class FoodAdditive(ChemicalEntity): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/FoodAdditive","biolink:FoodAdditive"]] = Field(["biolink:FoodAdditive"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2666,13 +2685,13 @@ class Food(ChemicalMixture): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Food","biolink:Food"]] = Field(["biolink:Food"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2698,17 +2717,17 @@ class Gene(GeneOrGeneProduct, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions. """ symbol: Optional[str] = Field(None, description="""Symbol for a particular thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Gene","biolink:Gene"]] = Field(["biolink:Gene"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2719,8 +2738,8 @@ class GeneProductMixin(GeneOrGeneProduct): """ The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules. """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") @@ -2728,8 +2747,8 @@ class GeneProductIsoformMixin(GeneProductMixin): """ This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms. """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") @@ -2741,13 +2760,13 @@ class MacromolecularComplex(MacromolecularMachineMixin, BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularComplex","biolink:MacromolecularComplex"]] = Field(["biolink:MacromolecularComplex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -2761,13 +2780,13 @@ class NucleosomeModification(GeneProductIsoformMixin, EpigenomicEntity, GenomicE in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleosomeModification","biolink:NucleosomeModification"]] = Field(["biolink:NucleosomeModification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2783,12 +2802,12 @@ class Genome(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Genome","biolink:Genome"]] = Field(["biolink:Genome"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2802,13 +2821,13 @@ class Exon(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Exon","biolink:Exon"]] = Field(["biolink:Exon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2822,13 +2841,13 @@ class Transcript(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Transcript","biolink:Transcript"]] = Field(["biolink:Transcript"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2840,13 +2859,13 @@ class CodingSequence(GenomicEntity, BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CodingSequence","biolink:CodingSequence"]] = Field(["biolink:CodingSequence"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2860,13 +2879,13 @@ class Polypeptide(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGe in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Polypeptide","biolink:Polypeptide"]] = Field(["biolink:Polypeptide"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2877,8 +2896,8 @@ class Protein(Polypeptide, GeneProductMixin): """ A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -2886,7 +2905,7 @@ class Protein(Polypeptide, GeneProductMixin): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Protein","biolink:Protein"]] = Field(["biolink:Protein"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2897,8 +2916,8 @@ class ProteinIsoform(Protein, GeneProductIsoformMixin): """ Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -2906,7 +2925,7 @@ class ProteinIsoform(Protein, GeneProductIsoformMixin): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinIsoform","biolink:ProteinIsoform"]] = Field(["biolink:ProteinIsoform"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2920,13 +2939,13 @@ class PosttranslationalModification(GeneProductIsoformMixin, BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PosttranslationalModification","biolink:PosttranslationalModification"]] = Field(["biolink:PosttranslationalModification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2940,13 +2959,13 @@ class NucleicAcidSequenceMotif(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleicAcidSequenceMotif","biolink:NucleicAcidSequenceMotif"]] = Field(["biolink:NucleicAcidSequenceMotif"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2954,8 +2973,8 @@ class NucleicAcidSequenceMotif(BiologicalEntity): class RNAProduct(Transcript, GeneProductMixin): - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -2963,7 +2982,7 @@ class RNAProduct(Transcript, GeneProductMixin): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RNAProduct","biolink:RNAProduct"]] = Field(["biolink:RNAProduct"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2974,8 +2993,8 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): """ Represents a protein that is a specific isoform of the canonical or reference RNA """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -2983,7 +3002,7 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RNAProductIsoform","biolink:RNAProductIsoform"]] = Field(["biolink:RNAProductIsoform"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2991,8 +3010,8 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): class NoncodingRNAProduct(RNAProduct): - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -3000,7 +3019,7 @@ class NoncodingRNAProduct(RNAProduct): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NoncodingRNAProduct","biolink:NoncodingRNAProduct"]] = Field(["biolink:NoncodingRNAProduct"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3008,8 +3027,8 @@ class NoncodingRNAProduct(RNAProduct): class MicroRNA(NoncodingRNAProduct): - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -3017,7 +3036,7 @@ class MicroRNA(NoncodingRNAProduct): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MicroRNA","biolink:MicroRNA"]] = Field(["biolink:MicroRNA"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3028,8 +3047,8 @@ class SiRNA(NoncodingRNAProduct): """ A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -3037,7 +3056,7 @@ class SiRNA(NoncodingRNAProduct): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SiRNA","biolink:SiRNA"]] = Field(["biolink:SiRNA"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3059,13 +3078,13 @@ class ProteinDomain(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinDomain","biolink:ProteinDomain"]] = Field(["biolink:ProteinDomain"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3077,13 +3096,13 @@ class ProteinFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinFamily","biolink:ProteinFamily"]] = Field(["biolink:ProteinFamily"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3098,13 +3117,13 @@ class GeneFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biologica in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneFamily","biolink:GeneFamily"]] = Field(["biolink:GeneFamily"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3119,11 +3138,11 @@ class Zygosity(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/Zygosity","biolink:Zygosity"]] = Field(["biolink:Zygosity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3139,12 +3158,12 @@ class Genotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Genotype","biolink:Genotype"]] = Field(["biolink:Genotype"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3160,12 +3179,12 @@ class Haplotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass) in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Haplotype","biolink:Haplotype"]] = Field(["biolink:Haplotype"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3182,12 +3201,12 @@ class SequenceVariant(GenomicEntity, BiologicalEntity, PhysicalEssence, Ontology in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceVariant","biolink:SequenceVariant"]] = Field(["biolink:SequenceVariant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3204,12 +3223,12 @@ class Snv(SequenceVariant): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Snv","biolink:Snv"]] = Field(["biolink:Snv"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3225,12 +3244,12 @@ class ReagentTargetedGene(GenomicEntity, BiologicalEntity, PhysicalEssence, Onto in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ReagentTargetedGene","biolink:ReagentTargetedGene"]] = Field(["biolink:ReagentTargetedGene"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3248,11 +3267,11 @@ class ClinicalAttribute(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalAttribute","biolink:ClinicalAttribute"]] = Field(["biolink:ClinicalAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3269,11 +3288,11 @@ class ClinicalMeasurement(ClinicalAttribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalMeasurement","biolink:ClinicalMeasurement"]] = Field(["biolink:ClinicalMeasurement"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3290,11 +3309,11 @@ class ClinicalModifier(ClinicalAttribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalModifier","biolink:ClinicalModifier"]] = Field(["biolink:ClinicalModifier"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3311,11 +3330,11 @@ class ClinicalCourse(ClinicalAttribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalCourse","biolink:ClinicalCourse"]] = Field(["biolink:ClinicalCourse"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3332,11 +3351,11 @@ class Onset(ClinicalCourse): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/Onset","biolink:Onset"]] = Field(["biolink:Onset"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3347,13 +3366,13 @@ class ClinicalEntity(NamedThing): Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalEntity","biolink:ClinicalEntity"]] = Field(["biolink:ClinicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3362,13 +3381,13 @@ class ClinicalEntity(NamedThing): class ClinicalTrial(ClinicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalTrial","biolink:ClinicalTrial"]] = Field(["biolink:ClinicalTrial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3377,13 +3396,13 @@ class ClinicalTrial(ClinicalEntity): class ClinicalIntervention(ClinicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalIntervention","biolink:ClinicalIntervention"]] = Field(["biolink:ClinicalIntervention"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3397,13 +3416,13 @@ class ClinicalFinding(PhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalFinding","biolink:ClinicalFinding"]] = Field(["biolink:ClinicalFinding"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3412,13 +3431,13 @@ class ClinicalFinding(PhenotypicFeature): class Hospitalization(ClinicalIntervention): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Hospitalization","biolink:Hospitalization"]] = Field(["biolink:Hospitalization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3436,11 +3455,11 @@ class SocioeconomicAttribute(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/SocioeconomicAttribute","biolink:SocioeconomicAttribute"]] = Field(["biolink:SocioeconomicAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3453,13 +3472,13 @@ class Case(IndividualOrganism, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Case","biolink:Case"]] = Field(["biolink:Case"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3473,13 +3492,13 @@ class Cohort(StudyPopulation, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Cohort","biolink:Cohort"]] = Field(["biolink:Cohort"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3510,11 +3529,11 @@ class GenomicBackgroundExposure(ExposureEvent, GeneGroupingMixin, GenomicEntity, has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/GenomicBackgroundExposure","biolink:GenomicBackgroundExposure"]] = Field(["biolink:GenomicBackgroundExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3538,12 +3557,12 @@ class PathologicalProcess(PathologicalEntityMixin, BiologicalProcess): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalProcess","biolink:PathologicalProcess"]] = Field(["biolink:PathologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3562,11 +3581,11 @@ class PathologicalProcessExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalProcessExposure","biolink:PathologicalProcessExposure"]] = Field(["biolink:PathologicalProcessExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3579,13 +3598,13 @@ class PathologicalAnatomicalStructure(PathologicalEntityMixin, AnatomicalEntity) in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalAnatomicalStructure","biolink:PathologicalAnatomicalStructure"]] = Field(["biolink:PathologicalAnatomicalStructure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3604,11 +3623,11 @@ class PathologicalAnatomicalExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalAnatomicalExposure","biolink:PathologicalAnatomicalExposure"]] = Field(["biolink:PathologicalAnatomicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3626,11 +3645,11 @@ class DiseaseOrPhenotypicFeatureExposure(PathologicalEntityMixin, ExposureEvent, iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureExposure","biolink:DiseaseOrPhenotypicFeatureExposure"]] = Field(["biolink:DiseaseOrPhenotypicFeatureExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3648,11 +3667,11 @@ class ChemicalExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalExposure","biolink:ChemicalExposure"]] = Field(["biolink:ChemicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3669,11 +3688,11 @@ class ComplexChemicalExposure(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ComplexChemicalExposure","biolink:ComplexChemicalExposure"]] = Field(["biolink:ComplexChemicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3691,11 +3710,11 @@ class DrugExposure(ChemicalExposure, ExposureEvent): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/DrugExposure","biolink:DrugExposure"]] = Field(["biolink:DrugExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3714,11 +3733,11 @@ class DrugToGeneInteractionExposure(DrugExposure, GeneGroupingMixin): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/DrugToGeneInteractionExposure","biolink:DrugToGeneInteractionExposure"]] = Field(["biolink:DrugToGeneInteractionExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3733,13 +3752,13 @@ class Treatment(ExposureEvent, NamedThing, ChemicalOrDrugOrTreatment): has_procedure: Optional[List[str]] = Field(None, description="""connects an entity to one or more (medical) procedures""") timepoint: Optional[str] = Field(None, description="""a point in time""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Treatment","biolink:Treatment"]] = Field(["biolink:Treatment"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3758,11 +3777,11 @@ class BioticExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/BioticExposure","biolink:BioticExposure"]] = Field(["biolink:BioticExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3780,11 +3799,11 @@ class EnvironmentalExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalExposure","biolink:EnvironmentalExposure"]] = Field(["biolink:EnvironmentalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3802,11 +3821,11 @@ class GeographicExposure(EnvironmentalExposure, ExposureEvent): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicExposure","biolink:GeographicExposure"]] = Field(["biolink:GeographicExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3824,11 +3843,11 @@ class BehavioralExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/BehavioralExposure","biolink:BehavioralExposure"]] = Field(["biolink:BehavioralExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3846,11 +3865,11 @@ class SocioeconomicExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/SocioeconomicExposure","biolink:SocioeconomicExposure"]] = Field(["biolink:SocioeconomicExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: List[str] = Field(..., description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3928,8 +3947,8 @@ class Association(Entity): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -3957,7 +3976,7 @@ class Association(Entity): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Association","biolink:Association"]] = Field(["biolink:Association"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3970,8 +3989,8 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -3999,7 +4018,7 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntityAssessesNamedThingAssociation","biolink:ChemicalEntityAssessesNamedThingAssociation"]] = Field(["biolink:ChemicalEntityAssessesNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4015,8 +4034,8 @@ class ContributorAssociation(Association): object: str = Field(..., description="""agent helping to realise the given entity (e.g. such as a publication)""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4044,7 +4063,7 @@ class ContributorAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ContributorAssociation","biolink:ContributorAssociation"]] = Field(["biolink:ContributorAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4060,8 +4079,8 @@ class GenotypeToGenotypePartAssociation(Association): object: str = Field(..., description="""child genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4089,7 +4108,7 @@ class GenotypeToGenotypePartAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToGenotypePartAssociation","biolink:GenotypeToGenotypePartAssociation"]] = Field(["biolink:GenotypeToGenotypePartAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4105,8 +4124,8 @@ class GenotypeToGeneAssociation(Association): object: str = Field(..., description="""gene implicated in genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4134,7 +4153,7 @@ class GenotypeToGeneAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToGeneAssociation","biolink:GenotypeToGeneAssociation"]] = Field(["biolink:GenotypeToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4150,8 +4169,8 @@ class GenotypeToVariantAssociation(Association): object: str = Field(..., description="""gene implicated in genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4179,7 +4198,7 @@ class GenotypeToVariantAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToVariantAssociation","biolink:GenotypeToVariantAssociation"]] = Field(["biolink:GenotypeToVariantAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4195,8 +4214,8 @@ class GeneToGeneAssociation(Association): object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4224,7 +4243,7 @@ class GeneToGeneAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneAssociation","biolink:GeneToGeneAssociation"]] = Field(["biolink:GeneToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4240,8 +4259,8 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4269,7 +4288,7 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneHomologyAssociation","biolink:GeneToGeneHomologyAssociation"]] = Field(["biolink:GeneToGeneHomologyAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4285,8 +4304,8 @@ class GeneToGeneFamilyAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4314,7 +4333,7 @@ class GeneToGeneFamilyAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneFamilyAssociation","biolink:GeneToGeneFamilyAssociation"]] = Field(["biolink:GeneToGeneFamilyAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4344,8 +4363,8 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4373,7 +4392,7 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneCoexpressionAssociation","biolink:GeneToGeneCoexpressionAssociation"]] = Field(["biolink:GeneToGeneCoexpressionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4389,8 +4408,8 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4418,7 +4437,7 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PairwiseGeneToGeneInteraction","biolink:PairwiseGeneToGeneInteraction"]] = Field(["biolink:PairwiseGeneToGeneInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4435,8 +4454,8 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4464,7 +4483,7 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): id: str = Field(..., description="""identifier for the interaction. This may come from an interaction database such as IMEX.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PairwiseMolecularInteraction","biolink:PairwiseMolecularInteraction"]] = Field(["biolink:PairwiseMolecularInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4525,8 +4544,8 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio object: str = Field(..., description="""the chemical element that is the target of the statement""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4554,7 +4573,7 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToChemicalAssociation","biolink:ChemicalToChemicalAssociation"]] = Field(["biolink:ChemicalToChemicalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4570,8 +4589,8 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): object: str = Field(..., description="""the chemical element that is the target of the statement""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4599,7 +4618,7 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ReactionToParticipantAssociation","biolink:ReactionToParticipantAssociation"]] = Field(["biolink:ReactionToParticipantAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4615,8 +4634,8 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): object: str = Field(..., description="""the chemical element that is the target of the statement""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4644,7 +4663,7 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ReactionToCatalystAssociation","biolink:ReactionToCatalystAssociation"]] = Field(["biolink:ReactionToCatalystAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4661,8 +4680,8 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): object: str = Field(..., description="""the downstream chemical entity""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4690,7 +4709,7 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToChemicalDerivationAssociation","biolink:ChemicalToChemicalDerivationAssociation"]] = Field(["biolink:ChemicalToChemicalDerivationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4706,8 +4725,8 @@ class MolecularActivityToPathwayAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4735,7 +4754,7 @@ class MolecularActivityToPathwayAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToPathwayAssociation","biolink:MolecularActivityToPathwayAssociation"]] = Field(["biolink:MolecularActivityToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4751,8 +4770,8 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association object: str = Field(..., description="""the pathway that is affected by the chemical""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4780,7 +4799,7 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToPathwayAssociation","biolink:ChemicalToPathwayAssociation"]] = Field(["biolink:ChemicalToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4798,8 +4817,8 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): population_context_qualifier: Optional[str] = Field(None, description="""a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4827,7 +4846,7 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NamedThingAssociatedWithLikelihoodOfNamedThingAssociation","biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation"]] = Field(["biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4851,8 +4870,8 @@ class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Assoc object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4880,7 +4899,7 @@ class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Assoc id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalGeneInteractionAssociation","biolink:ChemicalGeneInteractionAssociation"]] = Field(["biolink:ChemicalGeneInteractionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4900,8 +4919,8 @@ class GeneRegulatesGeneAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4929,7 +4948,7 @@ class GeneRegulatesGeneAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneRegulatesGeneAssociation","biolink:GeneRegulatesGeneAssociation"]] = Field(["biolink:GeneRegulatesGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4945,8 +4964,8 @@ class ProcessRegulatesProcessAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4974,7 +4993,7 @@ class ProcessRegulatesProcessAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProcessRegulatesProcessAssociation","biolink:ProcessRegulatesProcessAssociation"]] = Field(["biolink:ProcessRegulatesProcessAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5005,8 +5024,8 @@ class ChemicalAffectsGeneAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5034,7 +5053,7 @@ class ChemicalAffectsGeneAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalAffectsGeneAssociation","biolink:ChemicalAffectsGeneAssociation"]] = Field(["biolink:ChemicalAffectsGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5066,8 +5085,8 @@ class GeneAffectsChemicalAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5095,7 +5114,7 @@ class GeneAffectsChemicalAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneAffectsChemicalAssociation","biolink:GeneAffectsChemicalAssociation"]] = Field(["biolink:GeneAffectsChemicalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5111,8 +5130,8 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): object: str = Field(..., description="""the gene or gene product that is affected by the drug""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5140,7 +5159,7 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DrugToGeneAssociation","biolink:DrugToGeneAssociation"]] = Field(["biolink:DrugToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5165,8 +5184,8 @@ class MaterialSampleDerivationAssociation(Association): object: str = Field(..., description="""the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5194,7 +5213,7 @@ class MaterialSampleDerivationAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MaterialSampleDerivationAssociation","biolink:MaterialSampleDerivationAssociation"]] = Field(["biolink:MaterialSampleDerivationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5225,8 +5244,8 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5254,7 +5273,7 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseToExposureEventAssociation","biolink:DiseaseToExposureEventAssociation"]] = Field(["biolink:DiseaseToExposureEventAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5281,8 +5300,8 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Associa object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5310,7 +5329,7 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Associa id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ExposureEventToOutcomeAssociation","biolink:ExposureEventToOutcomeAssociation"]] = Field(["biolink:ExposureEventToOutcomeAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5401,8 +5420,8 @@ class PhenotypicFeatureToPhenotypicFeatureAssociation(PhenotypicFeatureToEntityA object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5430,7 +5449,7 @@ class PhenotypicFeatureToPhenotypicFeatureAssociation(PhenotypicFeatureToEntityA id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicFeatureToPhenotypicFeatureAssociation","biolink:PhenotypicFeatureToPhenotypicFeatureAssociation"]] = Field(["biolink:PhenotypicFeatureToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5456,8 +5475,8 @@ class InformationContentEntityToNamedThingAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5485,7 +5504,7 @@ class InformationContentEntityToNamedThingAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/InformationContentEntityToNamedThingAssociation","biolink:InformationContentEntityToNamedThingAssociation"]] = Field(["biolink:InformationContentEntityToNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5522,8 +5541,8 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature object: str = Field(..., description="""anatomical entity in which the disease or feature is found.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5551,7 +5570,7 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToLocationAssociation","biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"]] = Field(["biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5567,8 +5586,8 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenoty object: str = Field(..., description="""genetic inheritance associated with the specified disease or phenotypic feature.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5596,7 +5615,7 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenoty id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation","biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"]] = Field(["biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5618,8 +5637,8 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi object: str = Field(..., description="""disease or phenotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5647,7 +5666,7 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellLineToDiseaseOrPhenotypicFeatureAssociation","biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5663,8 +5682,8 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi object: str = Field(..., description="""the disease or phenotype that is affected by the chemical""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5692,7 +5711,7 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5709,8 +5728,8 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToD object: str = Field(..., description="""disease or phenotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5738,7 +5757,7 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToD id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5755,8 +5774,8 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C FDA_adverse_event_level: Optional[FDAIDAAdverseEventEnum] = Field(None) negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5784,7 +5803,7 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5800,8 +5819,8 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe object: str = Field(..., description="""disease or phenotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5829,7 +5848,7 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MaterialSampleToDiseaseOrPhenotypicFeatureAssociation","biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5852,8 +5871,8 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5881,7 +5900,7 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToPhenotypicFeatureAssociation","biolink:GenotypeToPhenotypicFeatureAssociation"]] = Field(["biolink:GenotypeToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5908,8 +5927,8 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5937,7 +5956,7 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ExposureEventToPhenotypicFeatureAssociation","biolink:ExposureEventToPhenotypicFeatureAssociation"]] = Field(["biolink:ExposureEventToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5969,8 +5988,8 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5998,7 +6017,7 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseToPhenotypicFeatureAssociation","biolink:DiseaseToPhenotypicFeatureAssociation"]] = Field(["biolink:DiseaseToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6021,8 +6040,8 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6050,7 +6069,7 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CaseToPhenotypicFeatureAssociation","biolink:CaseToPhenotypicFeatureAssociation"]] = Field(["biolink:CaseToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6077,8 +6096,8 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6106,7 +6125,7 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BehaviorToBehavioralFeatureAssociation","biolink:BehaviorToBehavioralFeatureAssociation"]] = Field(["biolink:BehaviorToBehavioralFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6138,8 +6157,8 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): object: str = Field(..., description="""the pathway that includes or is affected by the gene or gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6167,7 +6186,7 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToPathwayAssociation","biolink:GeneToPathwayAssociation"]] = Field(["biolink:GeneToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6189,8 +6208,8 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6218,7 +6237,7 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation","biolink:GeneToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:GeneToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6242,8 +6261,8 @@ class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssocia object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None, description="""Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6271,7 +6290,7 @@ class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssocia id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToPhenotypicFeatureAssociation","biolink:GeneToPhenotypicFeatureAssociation"]] = Field(["biolink:GeneToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6295,8 +6314,8 @@ class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, Gene sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6324,7 +6343,7 @@ class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, Gene id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToDiseaseAssociation","biolink:GeneToDiseaseAssociation"]] = Field(["biolink:GeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6348,8 +6367,8 @@ class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssoc sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6377,7 +6396,7 @@ class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssoc id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation","biolink:CausalGeneToDiseaseAssociation"]] = Field(["biolink:CausalGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6401,8 +6420,8 @@ class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityA sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6430,7 +6449,7 @@ class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityA id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation","biolink:CorrelatedGeneToDiseaseAssociation"]] = Field(["biolink:CorrelatedGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6454,8 +6473,8 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[DruggableGeneCategoryEnum]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6483,7 +6502,7 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DruggableGeneToDiseaseAssociation","biolink:DruggableGeneToDiseaseAssociation"]] = Field(["biolink:DruggableGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6505,8 +6524,8 @@ class PhenotypicFeatureToDiseaseAssociation(EntityToDiseaseAssociationMixin, Phe object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6534,7 +6553,7 @@ class PhenotypicFeatureToDiseaseAssociation(EntityToDiseaseAssociationMixin, Phe id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicFeatureToDiseaseAssociation","biolink:PhenotypicFeatureToDiseaseAssociation"]] = Field(["biolink:PhenotypicFeatureToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6560,8 +6579,8 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6589,7 +6608,7 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToGeneAssociation","biolink:VariantToGeneAssociation"]] = Field(["biolink:VariantToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6609,8 +6628,8 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6638,7 +6657,7 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToGeneExpressionAssociation","biolink:VariantToGeneExpressionAssociation"]] = Field(["biolink:VariantToGeneExpressionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6659,8 +6678,8 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6688,7 +6707,7 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToPopulationAssociation","biolink:VariantToPopulationAssociation"]] = Field(["biolink:VariantToPopulationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6704,8 +6723,8 @@ class PopulationToPopulationAssociation(Association): object: str = Field(..., description="""the population that form the object of the association""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6733,7 +6752,7 @@ class PopulationToPopulationAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PopulationToPopulationAssociation","biolink:PopulationToPopulationAssociation"]] = Field(["biolink:PopulationToPopulationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6747,8 +6766,8 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6776,7 +6795,7 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToPhenotypicFeatureAssociation","biolink:VariantToPhenotypicFeatureAssociation"]] = Field(["biolink:VariantToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6799,8 +6818,8 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea object: str = Field(..., description="""a disease that is associated with that variant""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6828,7 +6847,7 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToDiseaseAssociation","biolink:VariantToDiseaseAssociation"]] = Field(["biolink:VariantToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6847,8 +6866,8 @@ class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDis object: str = Field(..., description="""a disease that is associated with that genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6876,7 +6895,7 @@ class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDis id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToDiseaseAssociation","biolink:GenotypeToDiseaseAssociation"]] = Field(["biolink:GenotypeToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6907,8 +6926,8 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6936,7 +6955,7 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneAsAModelOfDiseaseAssociation","biolink:GeneAsAModelOfDiseaseAssociation"]] = Field(["biolink:GeneAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6957,8 +6976,8 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6986,7 +7005,7 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantAsAModelOfDiseaseAssociation","biolink:VariantAsAModelOfDiseaseAssociation"]] = Field(["biolink:VariantAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7005,8 +7024,8 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7034,7 +7053,7 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeAsAModelOfDiseaseAssociation","biolink:GenotypeAsAModelOfDiseaseAssociation"]] = Field(["biolink:GenotypeAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7053,8 +7072,8 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7082,7 +7101,7 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellLineAsAModelOfDiseaseAssociation","biolink:CellLineAsAModelOfDiseaseAssociation"]] = Field(["biolink:CellLineAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7101,8 +7120,8 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7130,7 +7149,7 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismalEntityAsAModelOfDiseaseAssociation","biolink:OrganismalEntityAsAModelOfDiseaseAssociation"]] = Field(["biolink:OrganismalEntityAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7149,8 +7168,8 @@ class OrganismToOrganismAssociation(Association): object: str = Field(..., description="""An association between two individual organisms.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7178,7 +7197,7 @@ class OrganismToOrganismAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismToOrganismAssociation","biolink:OrganismToOrganismAssociation"]] = Field(["biolink:OrganismToOrganismAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7191,8 +7210,8 @@ class TaxonToTaxonAssociation(Association): object: str = Field(..., description="""An association between individuals of different taxa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7220,7 +7239,7 @@ class TaxonToTaxonAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TaxonToTaxonAssociation","biolink:TaxonToTaxonAssociation"]] = Field(["biolink:TaxonToTaxonAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7237,8 +7256,8 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7266,7 +7285,7 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneHasVariantThatContributesToDiseaseAssociation","biolink:GeneHasVariantThatContributesToDiseaseAssociation"]] = Field(["biolink:GeneHasVariantThatContributesToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7292,8 +7311,8 @@ class GeneToExpressionSiteAssociation(Association): object: str = Field(..., description="""location in which the gene is expressed""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7321,7 +7340,7 @@ class GeneToExpressionSiteAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToExpressionSiteAssociation","biolink:GeneToExpressionSiteAssociation"]] = Field(["biolink:GeneToExpressionSiteAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7337,8 +7356,8 @@ class SequenceVariantModulatesTreatmentAssociation(Association): object: str = Field(..., description="""treatment whose efficacy is modulated by the subject variant""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7366,7 +7385,7 @@ class SequenceVariantModulatesTreatmentAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceVariantModulatesTreatmentAssociation","biolink:SequenceVariantModulatesTreatmentAssociation"]] = Field(["biolink:SequenceVariantModulatesTreatmentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7382,8 +7401,8 @@ class FunctionalAssociation(Association): object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7411,7 +7430,7 @@ class FunctionalAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/FunctionalAssociation","biolink:FunctionalAssociation"]] = Field(["biolink:FunctionalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7436,8 +7455,8 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7465,7 +7484,7 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToMolecularActivityAssociation","biolink:MacromolecularMachineToMolecularActivityAssociation"]] = Field(["biolink:MacromolecularMachineToMolecularActivityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7481,8 +7500,8 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7510,7 +7529,7 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToBiologicalProcessAssociation","biolink:MacromolecularMachineToBiologicalProcessAssociation"]] = Field(["biolink:MacromolecularMachineToBiologicalProcessAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7526,8 +7545,8 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7555,7 +7574,7 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToCellularComponentAssociation","biolink:MacromolecularMachineToCellularComponentAssociation"]] = Field(["biolink:MacromolecularMachineToCellularComponentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7571,8 +7590,8 @@ class MolecularActivityToChemicalEntityAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7600,7 +7619,7 @@ class MolecularActivityToChemicalEntityAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToChemicalEntityAssociation","biolink:MolecularActivityToChemicalEntityAssociation"]] = Field(["biolink:MolecularActivityToChemicalEntityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7616,8 +7635,8 @@ class MolecularActivityToMolecularActivityAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7645,7 +7664,7 @@ class MolecularActivityToMolecularActivityAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToMolecularActivityAssociation","biolink:MolecularActivityToMolecularActivityAssociation"]] = Field(["biolink:MolecularActivityToMolecularActivityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7658,8 +7677,8 @@ class GeneToGoTermAssociation(FunctionalAssociation): object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7687,7 +7706,7 @@ class GeneToGoTermAssociation(FunctionalAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGoTermAssociation","biolink:GeneToGoTermAssociation"]] = Field(["biolink:GeneToGoTermAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7702,8 +7721,8 @@ class EntityToDiseaseAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7731,7 +7750,7 @@ class EntityToDiseaseAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EntityToDiseaseAssociation","biolink:EntityToDiseaseAssociation"]] = Field(["biolink:EntityToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7746,8 +7765,8 @@ class EntityToPhenotypicFeatureAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7775,7 +7794,7 @@ class EntityToPhenotypicFeatureAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociation","biolink:EntityToPhenotypicFeatureAssociation"]] = Field(["biolink:EntityToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7791,8 +7810,8 @@ class SequenceAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7820,7 +7839,7 @@ class SequenceAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceAssociation","biolink:SequenceAssociation"]] = Field(["biolink:SequenceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7841,8 +7860,8 @@ class GenomicSequenceLocalization(SequenceAssociation): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7870,7 +7889,7 @@ class GenomicSequenceLocalization(SequenceAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenomicSequenceLocalization","biolink:GenomicSequenceLocalization"]] = Field(["biolink:GenomicSequenceLocalization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7886,8 +7905,8 @@ class SequenceFeatureRelationship(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7915,7 +7934,7 @@ class SequenceFeatureRelationship(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceFeatureRelationship","biolink:SequenceFeatureRelationship"]] = Field(["biolink:SequenceFeatureRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7931,8 +7950,8 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7960,7 +7979,7 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TranscriptToGeneRelationship","biolink:TranscriptToGeneRelationship"]] = Field(["biolink:TranscriptToGeneRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7976,8 +7995,8 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8005,7 +8024,7 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneProductRelationship","biolink:GeneToGeneProductRelationship"]] = Field(["biolink:GeneToGeneProductRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8021,8 +8040,8 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8050,7 +8069,7 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ExonToTranscriptRelationship","biolink:ExonToTranscriptRelationship"]] = Field(["biolink:ExonToTranscriptRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8067,8 +8086,8 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8096,7 +8115,7 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation","biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation"]] = Field(["biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8109,8 +8128,8 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8138,7 +8157,7 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityAssociation","biolink:AnatomicalEntityToAnatomicalEntityAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8154,8 +8173,8 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat object: str = Field(..., description="""the whole""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8183,7 +8202,7 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityPartOfAssociation","biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8199,8 +8218,8 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA object: str = Field(..., description="""the structure at an earlier time""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8228,7 +8247,7 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityOntogenicAssociation","biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8253,8 +8272,8 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8282,7 +8301,7 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation","biolink:OrganismTaxonToOrganismTaxonAssociation"]] = Field(["biolink:OrganismTaxonToOrganismTaxonAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8298,8 +8317,8 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss object: str = Field(..., description="""the more general taxon""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8327,7 +8346,7 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonSpecialization","biolink:OrganismTaxonToOrganismTaxonSpecialization"]] = Field(["biolink:OrganismTaxonToOrganismTaxonSpecialization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8344,8 +8363,8 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci object: str = Field(..., description="""the taxon that is the subject of the association""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8373,7 +8392,7 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonInteraction","biolink:OrganismTaxonToOrganismTaxonInteraction"]] = Field(["biolink:OrganismTaxonToOrganismTaxonInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8386,8 +8405,8 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As object: str = Field(..., description="""the environment in which the organism occurs""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8415,321 +8434,321 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToEnvironmentAssociation","biolink:OrganismTaxonToEnvironmentAssociation"]] = Field(["biolink:OrganismTaxonToEnvironmentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") - name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") - has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -MappingCollection.update_forward_refs() -PredicateMapping.update_forward_refs() -OntologyClass.update_forward_refs() -Annotation.update_forward_refs() -QuantityValue.update_forward_refs() -RelationshipQuantifier.update_forward_refs() -SensitivityQuantifier.update_forward_refs() -SpecificityQuantifier.update_forward_refs() -PathognomonicityQuantifier.update_forward_refs() -FrequencyQuantifier.update_forward_refs() -ChemicalOrDrugOrTreatment.update_forward_refs() -Entity.update_forward_refs() -NamedThing.update_forward_refs() -Attribute.update_forward_refs() -ChemicalRole.update_forward_refs() -BiologicalSex.update_forward_refs() -PhenotypicSex.update_forward_refs() -GenotypicSex.update_forward_refs() -SeverityValue.update_forward_refs() -RelationshipType.update_forward_refs() -TaxonomicRank.update_forward_refs() -OrganismTaxon.update_forward_refs() -Event.update_forward_refs() -AdministrativeEntity.update_forward_refs() -Agent.update_forward_refs() -InformationContentEntity.update_forward_refs() -StudyResult.update_forward_refs() -StudyVariable.update_forward_refs() -CommonDataElement.update_forward_refs() -ConceptCountAnalysisResult.update_forward_refs() -ObservedExpectedFrequencyAnalysisResult.update_forward_refs() -RelativeFrequencyAnalysisResult.update_forward_refs() -TextMiningResult.update_forward_refs() -ChiSquaredAnalysisResult.update_forward_refs() -LogOddsAnalysisResult.update_forward_refs() -Dataset.update_forward_refs() -DatasetDistribution.update_forward_refs() -DatasetVersion.update_forward_refs() -DatasetSummary.update_forward_refs() -ConfidenceLevel.update_forward_refs() -EvidenceType.update_forward_refs() -Publication.update_forward_refs() -Book.update_forward_refs() -BookChapter.update_forward_refs() -Serial.update_forward_refs() -Article.update_forward_refs() -JournalArticle.update_forward_refs() -Patent.update_forward_refs() -WebPage.update_forward_refs() -PreprintPublication.update_forward_refs() -DrugLabel.update_forward_refs() -RetrievalSource.update_forward_refs() -PhysicalEssenceOrOccurrent.update_forward_refs() -PhysicalEssence.update_forward_refs() -PhysicalEntity.update_forward_refs() -Occurrent.update_forward_refs() -ActivityAndBehavior.update_forward_refs() -Activity.update_forward_refs() -Study.update_forward_refs() -Procedure.update_forward_refs() -Phenomenon.update_forward_refs() -Device.update_forward_refs() -DiagnosticAid.update_forward_refs() -SubjectOfInvestigation.update_forward_refs() -MaterialSample.update_forward_refs() -PlanetaryEntity.update_forward_refs() -EnvironmentalProcess.update_forward_refs() -EnvironmentalFeature.update_forward_refs() -GeographicLocation.update_forward_refs() -GeographicLocationAtTime.update_forward_refs() -ThingWithTaxon.update_forward_refs() -BiologicalEntity.update_forward_refs() -GenomicEntity.update_forward_refs() -EpigenomicEntity.update_forward_refs() -BiologicalProcessOrActivity.update_forward_refs() -MolecularActivity.update_forward_refs() -BiologicalProcess.update_forward_refs() -Pathway.update_forward_refs() -PhysiologicalProcess.update_forward_refs() -Behavior.update_forward_refs() -OrganismAttribute.update_forward_refs() -PhenotypicQuality.update_forward_refs() -GeneticInheritance.update_forward_refs() -OrganismalEntity.update_forward_refs() -Bacterium.update_forward_refs() -Virus.update_forward_refs() -CellularOrganism.update_forward_refs() -Mammal.update_forward_refs() -Human.update_forward_refs() -Plant.update_forward_refs() -Invertebrate.update_forward_refs() -Vertebrate.update_forward_refs() -Fungus.update_forward_refs() -LifeStage.update_forward_refs() -IndividualOrganism.update_forward_refs() -PopulationOfIndividualOrganisms.update_forward_refs() -StudyPopulation.update_forward_refs() -DiseaseOrPhenotypicFeature.update_forward_refs() -Disease.update_forward_refs() -PhenotypicFeature.update_forward_refs() -BehavioralFeature.update_forward_refs() -AnatomicalEntity.update_forward_refs() -CellularComponent.update_forward_refs() -Cell.update_forward_refs() -CellLine.update_forward_refs() -GrossAnatomicalStructure.update_forward_refs() -ChemicalEntityOrGeneOrGeneProduct.update_forward_refs() -RegulatoryRegion.update_forward_refs() -AccessibleDnaRegion.update_forward_refs() -TranscriptionFactorBindingSite.update_forward_refs() -ChemicalEntityOrProteinOrPolypeptide.update_forward_refs() -ChemicalEntity.update_forward_refs() -MolecularEntity.update_forward_refs() -SmallMolecule.update_forward_refs() -ChemicalMixture.update_forward_refs() -NucleicAcidEntity.update_forward_refs() -MolecularMixture.update_forward_refs() -ComplexMolecularMixture.update_forward_refs() -ProcessedMaterial.update_forward_refs() -Drug.update_forward_refs() -EnvironmentalFoodContaminant.update_forward_refs() -FoodAdditive.update_forward_refs() -Food.update_forward_refs() -MacromolecularMachineMixin.update_forward_refs() -GeneOrGeneProduct.update_forward_refs() -Gene.update_forward_refs() -GeneProductMixin.update_forward_refs() -GeneProductIsoformMixin.update_forward_refs() -MacromolecularComplex.update_forward_refs() -NucleosomeModification.update_forward_refs() -Genome.update_forward_refs() -Exon.update_forward_refs() -Transcript.update_forward_refs() -CodingSequence.update_forward_refs() -Polypeptide.update_forward_refs() -Protein.update_forward_refs() -ProteinIsoform.update_forward_refs() -PosttranslationalModification.update_forward_refs() -NucleicAcidSequenceMotif.update_forward_refs() -RNAProduct.update_forward_refs() -RNAProductIsoform.update_forward_refs() -NoncodingRNAProduct.update_forward_refs() -MicroRNA.update_forward_refs() -SiRNA.update_forward_refs() -GeneGroupingMixin.update_forward_refs() -ProteinDomain.update_forward_refs() -ProteinFamily.update_forward_refs() -GeneFamily.update_forward_refs() -Zygosity.update_forward_refs() -Genotype.update_forward_refs() -Haplotype.update_forward_refs() -SequenceVariant.update_forward_refs() -Snv.update_forward_refs() -ReagentTargetedGene.update_forward_refs() -ClinicalAttribute.update_forward_refs() -ClinicalMeasurement.update_forward_refs() -ClinicalModifier.update_forward_refs() -ClinicalCourse.update_forward_refs() -Onset.update_forward_refs() -ClinicalEntity.update_forward_refs() -ClinicalTrial.update_forward_refs() -ClinicalIntervention.update_forward_refs() -ClinicalFinding.update_forward_refs() -Hospitalization.update_forward_refs() -SocioeconomicAttribute.update_forward_refs() -Case.update_forward_refs() -Cohort.update_forward_refs() -ExposureEvent.update_forward_refs() -GenomicBackgroundExposure.update_forward_refs() -PathologicalEntityMixin.update_forward_refs() -PathologicalProcess.update_forward_refs() -PathologicalProcessExposure.update_forward_refs() -PathologicalAnatomicalStructure.update_forward_refs() -PathologicalAnatomicalExposure.update_forward_refs() -DiseaseOrPhenotypicFeatureExposure.update_forward_refs() -ChemicalExposure.update_forward_refs() -ComplexChemicalExposure.update_forward_refs() -DrugExposure.update_forward_refs() -DrugToGeneInteractionExposure.update_forward_refs() -Treatment.update_forward_refs() -BioticExposure.update_forward_refs() -EnvironmentalExposure.update_forward_refs() -GeographicExposure.update_forward_refs() -BehavioralExposure.update_forward_refs() -SocioeconomicExposure.update_forward_refs() -Outcome.update_forward_refs() -PathologicalProcessOutcome.update_forward_refs() -PathologicalAnatomicalOutcome.update_forward_refs() -DiseaseOrPhenotypicFeatureOutcome.update_forward_refs() -BehavioralOutcome.update_forward_refs() -HospitalizationOutcome.update_forward_refs() -MortalityOutcome.update_forward_refs() -EpidemiologicalOutcome.update_forward_refs() -SocioeconomicOutcome.update_forward_refs() -Association.update_forward_refs() -ChemicalEntityAssessesNamedThingAssociation.update_forward_refs() -ContributorAssociation.update_forward_refs() -GenotypeToGenotypePartAssociation.update_forward_refs() -GenotypeToGeneAssociation.update_forward_refs() -GenotypeToVariantAssociation.update_forward_refs() -GeneToGeneAssociation.update_forward_refs() -GeneToGeneHomologyAssociation.update_forward_refs() -GeneToGeneFamilyAssociation.update_forward_refs() -GeneExpressionMixin.update_forward_refs() -GeneToGeneCoexpressionAssociation.update_forward_refs() -PairwiseGeneToGeneInteraction.update_forward_refs() -PairwiseMolecularInteraction.update_forward_refs() -CellLineToEntityAssociationMixin.update_forward_refs() -ChemicalEntityToEntityAssociationMixin.update_forward_refs() -DrugToEntityAssociationMixin.update_forward_refs() -ChemicalToEntityAssociationMixin.update_forward_refs() -CaseToEntityAssociationMixin.update_forward_refs() -ChemicalToChemicalAssociation.update_forward_refs() -ReactionToParticipantAssociation.update_forward_refs() -ReactionToCatalystAssociation.update_forward_refs() -ChemicalToChemicalDerivationAssociation.update_forward_refs() -MolecularActivityToPathwayAssociation.update_forward_refs() -ChemicalToPathwayAssociation.update_forward_refs() -NamedThingAssociatedWithLikelihoodOfNamedThingAssociation.update_forward_refs() -ChemicalGeneInteractionAssociation.update_forward_refs() -GeneRegulatesGeneAssociation.update_forward_refs() -ProcessRegulatesProcessAssociation.update_forward_refs() -ChemicalAffectsGeneAssociation.update_forward_refs() -GeneAffectsChemicalAssociation.update_forward_refs() -DrugToGeneAssociation.update_forward_refs() -MaterialSampleToEntityAssociationMixin.update_forward_refs() -MaterialSampleDerivationAssociation.update_forward_refs() -DiseaseToEntityAssociationMixin.update_forward_refs() -EntityToExposureEventAssociationMixin.update_forward_refs() -DiseaseToExposureEventAssociation.update_forward_refs() -EntityToOutcomeAssociationMixin.update_forward_refs() -ExposureEventToOutcomeAssociation.update_forward_refs() -FrequencyQualifierMixin.update_forward_refs() -EntityToFeatureOrDiseaseQualifiersMixin.update_forward_refs() -FeatureOrDiseaseQualifiersToEntityMixin.update_forward_refs() -EntityToPhenotypicFeatureAssociationMixin.update_forward_refs() -PhenotypicFeatureToEntityAssociationMixin.update_forward_refs() -PhenotypicFeatureToPhenotypicFeatureAssociation.update_forward_refs() -InformationContentEntityToNamedThingAssociation.update_forward_refs() -EntityToDiseaseAssociationMixin.update_forward_refs() -DiseaseOrPhenotypicFeatureToEntityAssociationMixin.update_forward_refs() -DiseaseOrPhenotypicFeatureToLocationAssociation.update_forward_refs() -DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation.update_forward_refs() -EntityToDiseaseOrPhenotypicFeatureAssociationMixin.update_forward_refs() -CellLineToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -ChemicalToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -MaterialSampleToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -GenotypeToEntityAssociationMixin.update_forward_refs() -GenotypeToPhenotypicFeatureAssociation.update_forward_refs() -ExposureEventToPhenotypicFeatureAssociation.update_forward_refs() -DiseaseToPhenotypicFeatureAssociation.update_forward_refs() -CaseToPhenotypicFeatureAssociation.update_forward_refs() -BehaviorToBehavioralFeatureAssociation.update_forward_refs() -GeneToEntityAssociationMixin.update_forward_refs() -GeneToPathwayAssociation.update_forward_refs() -VariantToEntityAssociationMixin.update_forward_refs() -GeneToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -GeneToPhenotypicFeatureAssociation.update_forward_refs() -GeneToDiseaseAssociation.update_forward_refs() -CausalGeneToDiseaseAssociation.update_forward_refs() -CorrelatedGeneToDiseaseAssociation.update_forward_refs() -DruggableGeneToDiseaseAssociation.update_forward_refs() -PhenotypicFeatureToDiseaseAssociation.update_forward_refs() -VariantToGeneAssociation.update_forward_refs() -VariantToGeneExpressionAssociation.update_forward_refs() -VariantToPopulationAssociation.update_forward_refs() -PopulationToPopulationAssociation.update_forward_refs() -VariantToPhenotypicFeatureAssociation.update_forward_refs() -VariantToDiseaseAssociation.update_forward_refs() -GenotypeToDiseaseAssociation.update_forward_refs() -ModelToDiseaseAssociationMixin.update_forward_refs() -GeneAsAModelOfDiseaseAssociation.update_forward_refs() -VariantAsAModelOfDiseaseAssociation.update_forward_refs() -GenotypeAsAModelOfDiseaseAssociation.update_forward_refs() -CellLineAsAModelOfDiseaseAssociation.update_forward_refs() -OrganismalEntityAsAModelOfDiseaseAssociation.update_forward_refs() -OrganismToOrganismAssociation.update_forward_refs() -TaxonToTaxonAssociation.update_forward_refs() -GeneHasVariantThatContributesToDiseaseAssociation.update_forward_refs() -GeneToExpressionSiteAssociation.update_forward_refs() -SequenceVariantModulatesTreatmentAssociation.update_forward_refs() -FunctionalAssociation.update_forward_refs() -MacromolecularMachineToEntityAssociationMixin.update_forward_refs() -MacromolecularMachineToMolecularActivityAssociation.update_forward_refs() -MacromolecularMachineToBiologicalProcessAssociation.update_forward_refs() -MacromolecularMachineToCellularComponentAssociation.update_forward_refs() -MolecularActivityToChemicalEntityAssociation.update_forward_refs() -MolecularActivityToMolecularActivityAssociation.update_forward_refs() -GeneToGoTermAssociation.update_forward_refs() -EntityToDiseaseAssociation.update_forward_refs() -EntityToPhenotypicFeatureAssociation.update_forward_refs() -SequenceAssociation.update_forward_refs() -GenomicSequenceLocalization.update_forward_refs() -SequenceFeatureRelationship.update_forward_refs() -TranscriptToGeneRelationship.update_forward_refs() -GeneToGeneProductRelationship.update_forward_refs() -ExonToTranscriptRelationship.update_forward_refs() -ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation.update_forward_refs() -AnatomicalEntityToAnatomicalEntityAssociation.update_forward_refs() -AnatomicalEntityToAnatomicalEntityPartOfAssociation.update_forward_refs() -AnatomicalEntityToAnatomicalEntityOntogenicAssociation.update_forward_refs() -OrganismTaxonToEntityAssociation.update_forward_refs() -OrganismTaxonToOrganismTaxonAssociation.update_forward_refs() -OrganismTaxonToOrganismTaxonSpecialization.update_forward_refs() -OrganismTaxonToOrganismTaxonInteraction.update_forward_refs() -OrganismTaxonToEnvironmentAssociation.update_forward_refs() + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") + + +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +MappingCollection.model_rebuild() +PredicateMapping.model_rebuild() +OntologyClass.model_rebuild() +Annotation.model_rebuild() +QuantityValue.model_rebuild() +RelationshipQuantifier.model_rebuild() +SensitivityQuantifier.model_rebuild() +SpecificityQuantifier.model_rebuild() +PathognomonicityQuantifier.model_rebuild() +FrequencyQuantifier.model_rebuild() +ChemicalOrDrugOrTreatment.model_rebuild() +Entity.model_rebuild() +NamedThing.model_rebuild() +Attribute.model_rebuild() +ChemicalRole.model_rebuild() +BiologicalSex.model_rebuild() +PhenotypicSex.model_rebuild() +GenotypicSex.model_rebuild() +SeverityValue.model_rebuild() +RelationshipType.model_rebuild() +TaxonomicRank.model_rebuild() +OrganismTaxon.model_rebuild() +Event.model_rebuild() +AdministrativeEntity.model_rebuild() +Agent.model_rebuild() +InformationContentEntity.model_rebuild() +StudyResult.model_rebuild() +StudyVariable.model_rebuild() +CommonDataElement.model_rebuild() +ConceptCountAnalysisResult.model_rebuild() +ObservedExpectedFrequencyAnalysisResult.model_rebuild() +RelativeFrequencyAnalysisResult.model_rebuild() +TextMiningResult.model_rebuild() +ChiSquaredAnalysisResult.model_rebuild() +LogOddsAnalysisResult.model_rebuild() +Dataset.model_rebuild() +DatasetDistribution.model_rebuild() +DatasetVersion.model_rebuild() +DatasetSummary.model_rebuild() +ConfidenceLevel.model_rebuild() +EvidenceType.model_rebuild() +Publication.model_rebuild() +Book.model_rebuild() +BookChapter.model_rebuild() +Serial.model_rebuild() +Article.model_rebuild() +JournalArticle.model_rebuild() +Patent.model_rebuild() +WebPage.model_rebuild() +PreprintPublication.model_rebuild() +DrugLabel.model_rebuild() +RetrievalSource.model_rebuild() +PhysicalEssenceOrOccurrent.model_rebuild() +PhysicalEssence.model_rebuild() +PhysicalEntity.model_rebuild() +Occurrent.model_rebuild() +ActivityAndBehavior.model_rebuild() +Activity.model_rebuild() +Study.model_rebuild() +Procedure.model_rebuild() +Phenomenon.model_rebuild() +Device.model_rebuild() +DiagnosticAid.model_rebuild() +SubjectOfInvestigation.model_rebuild() +MaterialSample.model_rebuild() +PlanetaryEntity.model_rebuild() +EnvironmentalProcess.model_rebuild() +EnvironmentalFeature.model_rebuild() +GeographicLocation.model_rebuild() +GeographicLocationAtTime.model_rebuild() +ThingWithTaxon.model_rebuild() +BiologicalEntity.model_rebuild() +GenomicEntity.model_rebuild() +EpigenomicEntity.model_rebuild() +BiologicalProcessOrActivity.model_rebuild() +MolecularActivity.model_rebuild() +BiologicalProcess.model_rebuild() +Pathway.model_rebuild() +PhysiologicalProcess.model_rebuild() +Behavior.model_rebuild() +OrganismAttribute.model_rebuild() +PhenotypicQuality.model_rebuild() +GeneticInheritance.model_rebuild() +OrganismalEntity.model_rebuild() +Bacterium.model_rebuild() +Virus.model_rebuild() +CellularOrganism.model_rebuild() +Mammal.model_rebuild() +Human.model_rebuild() +Plant.model_rebuild() +Invertebrate.model_rebuild() +Vertebrate.model_rebuild() +Fungus.model_rebuild() +LifeStage.model_rebuild() +IndividualOrganism.model_rebuild() +PopulationOfIndividualOrganisms.model_rebuild() +StudyPopulation.model_rebuild() +DiseaseOrPhenotypicFeature.model_rebuild() +Disease.model_rebuild() +PhenotypicFeature.model_rebuild() +BehavioralFeature.model_rebuild() +AnatomicalEntity.model_rebuild() +CellularComponent.model_rebuild() +Cell.model_rebuild() +CellLine.model_rebuild() +GrossAnatomicalStructure.model_rebuild() +ChemicalEntityOrGeneOrGeneProduct.model_rebuild() +RegulatoryRegion.model_rebuild() +AccessibleDnaRegion.model_rebuild() +TranscriptionFactorBindingSite.model_rebuild() +ChemicalEntityOrProteinOrPolypeptide.model_rebuild() +ChemicalEntity.model_rebuild() +MolecularEntity.model_rebuild() +SmallMolecule.model_rebuild() +ChemicalMixture.model_rebuild() +NucleicAcidEntity.model_rebuild() +MolecularMixture.model_rebuild() +ComplexMolecularMixture.model_rebuild() +ProcessedMaterial.model_rebuild() +Drug.model_rebuild() +EnvironmentalFoodContaminant.model_rebuild() +FoodAdditive.model_rebuild() +Food.model_rebuild() +MacromolecularMachineMixin.model_rebuild() +GeneOrGeneProduct.model_rebuild() +Gene.model_rebuild() +GeneProductMixin.model_rebuild() +GeneProductIsoformMixin.model_rebuild() +MacromolecularComplex.model_rebuild() +NucleosomeModification.model_rebuild() +Genome.model_rebuild() +Exon.model_rebuild() +Transcript.model_rebuild() +CodingSequence.model_rebuild() +Polypeptide.model_rebuild() +Protein.model_rebuild() +ProteinIsoform.model_rebuild() +PosttranslationalModification.model_rebuild() +NucleicAcidSequenceMotif.model_rebuild() +RNAProduct.model_rebuild() +RNAProductIsoform.model_rebuild() +NoncodingRNAProduct.model_rebuild() +MicroRNA.model_rebuild() +SiRNA.model_rebuild() +GeneGroupingMixin.model_rebuild() +ProteinDomain.model_rebuild() +ProteinFamily.model_rebuild() +GeneFamily.model_rebuild() +Zygosity.model_rebuild() +Genotype.model_rebuild() +Haplotype.model_rebuild() +SequenceVariant.model_rebuild() +Snv.model_rebuild() +ReagentTargetedGene.model_rebuild() +ClinicalAttribute.model_rebuild() +ClinicalMeasurement.model_rebuild() +ClinicalModifier.model_rebuild() +ClinicalCourse.model_rebuild() +Onset.model_rebuild() +ClinicalEntity.model_rebuild() +ClinicalTrial.model_rebuild() +ClinicalIntervention.model_rebuild() +ClinicalFinding.model_rebuild() +Hospitalization.model_rebuild() +SocioeconomicAttribute.model_rebuild() +Case.model_rebuild() +Cohort.model_rebuild() +ExposureEvent.model_rebuild() +GenomicBackgroundExposure.model_rebuild() +PathologicalEntityMixin.model_rebuild() +PathologicalProcess.model_rebuild() +PathologicalProcessExposure.model_rebuild() +PathologicalAnatomicalStructure.model_rebuild() +PathologicalAnatomicalExposure.model_rebuild() +DiseaseOrPhenotypicFeatureExposure.model_rebuild() +ChemicalExposure.model_rebuild() +ComplexChemicalExposure.model_rebuild() +DrugExposure.model_rebuild() +DrugToGeneInteractionExposure.model_rebuild() +Treatment.model_rebuild() +BioticExposure.model_rebuild() +EnvironmentalExposure.model_rebuild() +GeographicExposure.model_rebuild() +BehavioralExposure.model_rebuild() +SocioeconomicExposure.model_rebuild() +Outcome.model_rebuild() +PathologicalProcessOutcome.model_rebuild() +PathologicalAnatomicalOutcome.model_rebuild() +DiseaseOrPhenotypicFeatureOutcome.model_rebuild() +BehavioralOutcome.model_rebuild() +HospitalizationOutcome.model_rebuild() +MortalityOutcome.model_rebuild() +EpidemiologicalOutcome.model_rebuild() +SocioeconomicOutcome.model_rebuild() +Association.model_rebuild() +ChemicalEntityAssessesNamedThingAssociation.model_rebuild() +ContributorAssociation.model_rebuild() +GenotypeToGenotypePartAssociation.model_rebuild() +GenotypeToGeneAssociation.model_rebuild() +GenotypeToVariantAssociation.model_rebuild() +GeneToGeneAssociation.model_rebuild() +GeneToGeneHomologyAssociation.model_rebuild() +GeneToGeneFamilyAssociation.model_rebuild() +GeneExpressionMixin.model_rebuild() +GeneToGeneCoexpressionAssociation.model_rebuild() +PairwiseGeneToGeneInteraction.model_rebuild() +PairwiseMolecularInteraction.model_rebuild() +CellLineToEntityAssociationMixin.model_rebuild() +ChemicalEntityToEntityAssociationMixin.model_rebuild() +DrugToEntityAssociationMixin.model_rebuild() +ChemicalToEntityAssociationMixin.model_rebuild() +CaseToEntityAssociationMixin.model_rebuild() +ChemicalToChemicalAssociation.model_rebuild() +ReactionToParticipantAssociation.model_rebuild() +ReactionToCatalystAssociation.model_rebuild() +ChemicalToChemicalDerivationAssociation.model_rebuild() +MolecularActivityToPathwayAssociation.model_rebuild() +ChemicalToPathwayAssociation.model_rebuild() +NamedThingAssociatedWithLikelihoodOfNamedThingAssociation.model_rebuild() +ChemicalGeneInteractionAssociation.model_rebuild() +GeneRegulatesGeneAssociation.model_rebuild() +ProcessRegulatesProcessAssociation.model_rebuild() +ChemicalAffectsGeneAssociation.model_rebuild() +GeneAffectsChemicalAssociation.model_rebuild() +DrugToGeneAssociation.model_rebuild() +MaterialSampleToEntityAssociationMixin.model_rebuild() +MaterialSampleDerivationAssociation.model_rebuild() +DiseaseToEntityAssociationMixin.model_rebuild() +EntityToExposureEventAssociationMixin.model_rebuild() +DiseaseToExposureEventAssociation.model_rebuild() +EntityToOutcomeAssociationMixin.model_rebuild() +ExposureEventToOutcomeAssociation.model_rebuild() +FrequencyQualifierMixin.model_rebuild() +EntityToFeatureOrDiseaseQualifiersMixin.model_rebuild() +FeatureOrDiseaseQualifiersToEntityMixin.model_rebuild() +EntityToPhenotypicFeatureAssociationMixin.model_rebuild() +PhenotypicFeatureToEntityAssociationMixin.model_rebuild() +PhenotypicFeatureToPhenotypicFeatureAssociation.model_rebuild() +InformationContentEntityToNamedThingAssociation.model_rebuild() +EntityToDiseaseAssociationMixin.model_rebuild() +DiseaseOrPhenotypicFeatureToEntityAssociationMixin.model_rebuild() +DiseaseOrPhenotypicFeatureToLocationAssociation.model_rebuild() +DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation.model_rebuild() +EntityToDiseaseOrPhenotypicFeatureAssociationMixin.model_rebuild() +CellLineToDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +ChemicalToDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +MaterialSampleToDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +GenotypeToEntityAssociationMixin.model_rebuild() +GenotypeToPhenotypicFeatureAssociation.model_rebuild() +ExposureEventToPhenotypicFeatureAssociation.model_rebuild() +DiseaseToPhenotypicFeatureAssociation.model_rebuild() +CaseToPhenotypicFeatureAssociation.model_rebuild() +BehaviorToBehavioralFeatureAssociation.model_rebuild() +GeneToEntityAssociationMixin.model_rebuild() +GeneToPathwayAssociation.model_rebuild() +VariantToEntityAssociationMixin.model_rebuild() +GeneToDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +GeneToPhenotypicFeatureAssociation.model_rebuild() +GeneToDiseaseAssociation.model_rebuild() +CausalGeneToDiseaseAssociation.model_rebuild() +CorrelatedGeneToDiseaseAssociation.model_rebuild() +DruggableGeneToDiseaseAssociation.model_rebuild() +PhenotypicFeatureToDiseaseAssociation.model_rebuild() +VariantToGeneAssociation.model_rebuild() +VariantToGeneExpressionAssociation.model_rebuild() +VariantToPopulationAssociation.model_rebuild() +PopulationToPopulationAssociation.model_rebuild() +VariantToPhenotypicFeatureAssociation.model_rebuild() +VariantToDiseaseAssociation.model_rebuild() +GenotypeToDiseaseAssociation.model_rebuild() +ModelToDiseaseAssociationMixin.model_rebuild() +GeneAsAModelOfDiseaseAssociation.model_rebuild() +VariantAsAModelOfDiseaseAssociation.model_rebuild() +GenotypeAsAModelOfDiseaseAssociation.model_rebuild() +CellLineAsAModelOfDiseaseAssociation.model_rebuild() +OrganismalEntityAsAModelOfDiseaseAssociation.model_rebuild() +OrganismToOrganismAssociation.model_rebuild() +TaxonToTaxonAssociation.model_rebuild() +GeneHasVariantThatContributesToDiseaseAssociation.model_rebuild() +GeneToExpressionSiteAssociation.model_rebuild() +SequenceVariantModulatesTreatmentAssociation.model_rebuild() +FunctionalAssociation.model_rebuild() +MacromolecularMachineToEntityAssociationMixin.model_rebuild() +MacromolecularMachineToMolecularActivityAssociation.model_rebuild() +MacromolecularMachineToBiologicalProcessAssociation.model_rebuild() +MacromolecularMachineToCellularComponentAssociation.model_rebuild() +MolecularActivityToChemicalEntityAssociation.model_rebuild() +MolecularActivityToMolecularActivityAssociation.model_rebuild() +GeneToGoTermAssociation.model_rebuild() +EntityToDiseaseAssociation.model_rebuild() +EntityToPhenotypicFeatureAssociation.model_rebuild() +SequenceAssociation.model_rebuild() +GenomicSequenceLocalization.model_rebuild() +SequenceFeatureRelationship.model_rebuild() +TranscriptToGeneRelationship.model_rebuild() +GeneToGeneProductRelationship.model_rebuild() +ExonToTranscriptRelationship.model_rebuild() +ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation.model_rebuild() +AnatomicalEntityToAnatomicalEntityAssociation.model_rebuild() +AnatomicalEntityToAnatomicalEntityPartOfAssociation.model_rebuild() +AnatomicalEntityToAnatomicalEntityOntogenicAssociation.model_rebuild() +OrganismTaxonToEntityAssociation.model_rebuild() +OrganismTaxonToOrganismTaxonAssociation.model_rebuild() +OrganismTaxonToOrganismTaxonSpecialization.model_rebuild() +OrganismTaxonToOrganismTaxonInteraction.model_rebuild() +OrganismTaxonToEnvironmentAssociation.model_rebuild() diff --git a/src/biolink_model/schema/biolink_model.yaml b/src/biolink_model/schema/biolink_model.yaml index 2e8f43205..2abfaaec7 100644 --- a/src/biolink_model/schema/biolink_model.yaml +++ b/src/biolink_model/schema/biolink_model.yaml @@ -6138,7 +6138,6 @@ slots: range: KnowledgeLevelEnum multivalued: false required: true - ifabsent: string(not_provided) examples: - value: knowledge_assertion - value: prediction @@ -6166,7 +6165,6 @@ slots: range: AgentTypeEnum multivalued: false required: true - ifabsent: string(not_provided) examples: - value: manual_agent - value: automated_agent diff --git a/src/biolink_model/scripts/classprefixes.py b/src/biolink_model/scripts/classprefixes.py index b25847fb2..c11a30b12 100644 --- a/src/biolink_model/scripts/classprefixes.py +++ b/src/biolink_model/scripts/classprefixes.py @@ -1,5 +1,5 @@ # Auto generated from class_prefixes.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-10-10T17:39:55 +# Generation date: 2024-10-10T16:38:51 # Schema: BiolinkClassPrefixes # # id: biolink-model-class-prefixes @@ -11,7 +11,7 @@ from jsonasobj2 import JsonObj, as_dict from typing import Optional, List, Union, Dict, ClassVar, Any from dataclasses import dataclass -from datetime import date, datetime +from datetime import date, datetime, time from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions from linkml_runtime.utils.slot import Slot @@ -50,7 +50,7 @@ -@dataclass +@dataclass(repr=False) class BiolinkClassPrefixMap(YAMLRoot): """ preferred order identifier prefixes per class in Biolink Model @@ -76,7 +76,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class BiolinkClassPrefixesCollection(YAMLRoot): """ collection of BiolinkClassPrefixes objects @@ -98,7 +98,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class Prefix(YAMLRoot): _inherited_slots: ClassVar[List[str]] = []